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{ "count": 496, "next": "?page=2", "previous": null, "list": [ { "name": "BetAware", "description": "A software package for the analysis of TransMembrane β-barrel proteins.", "homepage": "http://betaware.biocomp.unibo.it/BetAware/default/index", "biotoolsID": "betaware", "biotoolsCURIE": "biotools:betaware", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "betaware-deep", "type": "hasNewVersion" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0267", "term": "Protein secondary structure prediction" }, { "uri": "http://edamontology.org/operation_0269", "term": "Transmembrane protein prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0889", "term": "Structural profile" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Prediction", "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" }, { "uri": "http://edamontology.org/topic_3542", "term": "Protein secondary structure" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [ { "url": "http://betaware.biocomp.unibo.it/BetAware/default/software", "type": "Source code", "note": null, "version": null }, { "url": "http://betaware.biocomp.unibo.it/BetAware/default/software", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://bioinformatics.oxfordjournals.org/content/29/4/504.abstract", "type": [ "Citation instructions" ], "note": null }, { "url": "http://betaware.biocomp.unibo.it/BetAware/default/software", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts728", "pmid": "23297037", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "BETAWARE: A machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes", "abstract": "The annotation of membrane proteins in proteomes is an important problem of Computational Biology, especially after the development of high-throughput techniques that allow fast and efficient genome sequencing. Among membrane proteins, transmembrane β-barrels (TMBBs) are poorly represented in the database of protein structures (PDB) and difficult to identify with experimental approaches. They are, however, extremely important, playing key roles in several cell functions and bacterial pathogenicity. TMBBs are included in the lipid bilayer with a β-barrel structure and are presently found in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. Recently, we developed two top-performing methods based on machine-learning approaches to tackle both the detection of TMBBs in sets of proteins and the prediction of their topology. Here, we present our BETAWARE program that includes both approaches and can run as a standalone program on a linux-based computer to easily address in-home massive protein annotation or filtering.Availability and implementation: http://www.biocomp.unibo.it/ ∼savojard/betawarecl. © 2013 The Author.", "date": "2013-02-15T00:00:00Z", "citationCount": 38, "authors": [ { "name": "Savojardo C." }, { "name": "Fariselli P." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bioinformatics/btr549", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines", "abstract": "Motivation: Transmembrane β-barrels (TMBBs) are extremely important proteins that play key roles in several cell functions. They cross the lipid bilayer with β-barrel structures. TMBBs are presently found in the outer membranes of Gram-negative bacteria and of mitochondria and chloroplasts. Loop exposure outside the bacterial cell membranes makes TMBBs important targets for vaccine or drug therapies. In genomes, they are not highly represented and are difficult to identify with experimental approaches. Several computational methods have been developed to discriminate TMBBs from other types of proteins. However, the best performing approaches have a high fraction of false positive predictions.Results: In this article, we introduce a new machine learning approach for TMBB detection based on N-to-1 Extreme Learning Machines that significantly outperforms previous methods achieving a Matthews correlation coefficient of 0.82, a probability of correct prediction of 0.92 and a sensitivity of 0.73. © The Author 2011. Published by Oxford University Press. All rights reserved.", "date": "2011-11-01T00:00:00Z", "citationCount": 19, "authors": [ { "name": "Savojardo C." }, { "name": "Fariselli P." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1186/1748-7188-4-13", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Grammatical-restrained hidden conditional random fields for bioinformatics applications", "abstract": "Background: Discriminative models are designed to naturally address classification tasks. However, some applications require the inclusion of grammar rules, and in these cases generative models, such as Hidden Markov Models (HMMs) and Stochastic Grammars, are routinely applied. Results: We introduce Grammatical-Restrained Hidden Conditional Random Fields (GRHCRFs) as an extension of Hidden Conditional Random Fields (HCRFs). GRHCRFs while preserving the discriminative character of HCRFs, can assign labels in agreement with the production rules of a defined grammar. The main GRHCRF novelty is the possibility of including in HCRFs prior knowledge of the problem by means of a defined grammar. Our current implementation allows regular grammar rules. We test our GRHCRF on a typical biosequence labeling problem: the prediction of the topology of Prokaryotic outer-membrane proteins. Conclusion: We show that in a typical biosequence labeling problem the GRHCRF performs better than CRF models of the same complexity, indicating that GRHCRFs can be useful tools for biosequence analysis applications. Availability: GRHCRF software is available under GPLv3 licence at the website. http://www.biocomp.unibo.it/~savojard/biocrf-0.9.tar.gz. © 2009 Fariselli et al; licensee BioMed Central Ltd.", "date": "2009-10-22T00:00:00Z", "citationCount": 18, "authors": [ { "name": "Fariselli P." }, { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Algorithms for Molecular Biology" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": "http://biocomp.unibo.it/savojard/", "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null } ], "community": null, "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2016-01-22T15:07:25Z", "lastUpdate": "2024-03-07T17:59:38.621240Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA", "savo" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "hictk", "description": "Blazing fast toolkit to work with .hic and .cool files", "homepage": "https://github.com/paulsengroup/hictk", "biotoolsID": "hictk", "biotoolsCURIE": "biotools:hictk", "version": [ "0.0.1", "0.0.2", "0.0.3", "0.0.4", "0.0.5", "0.0.6", "0.0.7", "0.0.8", "0.0.9", "0.0.10" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [], "license": "MIT", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/paulsengroup/hictk", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/paulsengroup/hictk/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/paulsengroup/hictk/releases", "type": "Downloads page", "note": null, "version": null }, { "url": "https://anaconda.org/bioconda/hictk", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/paulsengroup/hictk/pkgs/container/hictk", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://hictk.readthedocs.io/en/latest/index.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2023.11.26.568707", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [], "community": null, "owner": "robomics", "additionDate": "2024-02-02T14:42:46.030561Z", "lastUpdate": "2024-03-06T19:01:40.827908Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OmicsSuite", "description": "OmicsSuite (https://omicssuite.github.io, https://github.com/OmicsSuite/), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multi-omics (transcriptomics, genomics, protein omics, metabolomics, single cell), microbiology, clinical, etc.", "homepage": "https://github.com/OmicsSuite/", "biotoolsID": "omicssuite", "biotoolsCURIE": "biotools:omicssuite", "version": [ "1.4.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Analysis" }, { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1916", "term": "Alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" }, { "uri": "http://edamontology.org/format_2376", "term": "RDF format" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Desktop application", "Suite", "Bioinformatics portal", "Plug-in", "Web application", "Workbench", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3315", "term": "Mathematics" } ], "operatingSystem": [ "Windows" ], "language": [ "Java", "Python", "R", "JavaScript" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/OmicsSuite/", "type": [ "Repository" ], "note": "GitHub Organization" }, { "url": "https://omicssuite.github.io", "type": [ "Helpdesk" ], "note": "OmicsSuite Website" }, { "url": "https://space.bilibili.com/34105515", "type": [ "Social media" ], "note": "OmicsSuite Courses" }, { "url": "https://doi.org/10.1093/hr/uhad195", "type": [ "Helpdesk" ], "note": "OmicsSuite Paper" } ], "download": [ { "url": "https://omicssuite.github.io", "type": "Downloads page", "note": "GitHub download page", "version": "1.4.0" }, { "url": "https://sourceforge.net/projects/omicssuite-github-io/files/latest/download", "type": "Binaries", "note": "SourceForge download", "version": "1.4.0" }, { "url": "https://www.aliyundrive.com/s/Defuhf7FVGw", "type": "Binaries", "note": "ALiYun Drive", "version": "1.4.0" } ], "documentation": [], "publication": [ { "doi": "10.1093/hr/uhad195", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": "1.4.0", "note": "Ben-ben Miao, Wei Dong, Yi-xin Gu, Zhao-fang Han, Xuan Luo, Cai-huan Ke, Wei-wei You, OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data, Horticulture Research, 2023;, uhad195, https://doi.org/10.1093/hr/uhad195.", "metadata": { "title": "OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data", "abstract": "With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems; however, it is challenging for most experimental biologists to analyse data using command-line interfaces, coding, and scripting. Based on experience with multi-omics, we have developed OmicsSuite, a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization. The suite has 175 sub-applications in 12 categories, including Sequence, Statistics, Algorithm, Genomics, Transcriptomics, Enrichment, Proteomics, Metabolomics, Clinical, Microorganism, Single Cell, and Table Operation. We created the user interface with Sequence View, Table View, and intelligent components based on JavaFX and the popular Shiny framework. The multi-omics analysis functions were developed based on BioJava and 300+ packages provided by the R CRAN and Bioconductor communities, and it encompasses over 3000 adjustable parameter interfaces. OmicsSuite can directly read multi-omics raw data in FastA, FastQ, Mutation Annotation Format, mzML, Matrix, and HDF5 formats, and the programs emphasize data transfer directions and pipeline analysis functions. OmicsSuite can produce pre-publication images and tables, allowing users to focus on biological aspects. OmicsSuite offers multi-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in plants. It enables researchers to freely explore the molecular information contained in multi-omics big data (Source: https://github.com/OmicsSuite/, Website: https://omicssuite.github.io, v1.3.9).", "date": "2023-11-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Miao B.-B." }, { "name": "Dong W." }, { "name": "Gu Y.-X." }, { "name": "Han Z.-F." }, { "name": "Luo X." }, { "name": "Ke C.-H." }, { "name": "You W.-W." } ], "journal": "Horticulture Research" } } ], "credit": [], "community": null, "owner": "benben.miao", "additionDate": "2024-02-25T14:21:46.268659Z", "lastUpdate": "2024-02-25T14:22:11.738545Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "OmicsSuite", "description": "OmicsSuite (https://omicssuite.github.io, https://github.com/OmicsSuite/), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multi-omics (transcriptomics, genomics, protein omics, metabolomics, single cell), microbiology, clinical, etc.", "homepage": "https://github.com/OmicsSuite/", "biotoolsID": "bioscitools", "biotoolsCURIE": "biotools:bioscitools", "version": [ "1.4.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Analysis" }, { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1916", "term": "Alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" }, { "uri": "http://edamontology.org/format_2376", "term": "RDF format" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Desktop application", "Suite", "Bioinformatics portal", "Plug-in", "Web application", "Workbench", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3315", "term": "Mathematics" } ], "operatingSystem": [ "Windows" ], "language": [ "Java", "Python", "R", "JavaScript" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/OmicsSuite/", "type": [ "Repository" ], "note": "GitHub Organization" }, { "url": "https://omicssuite.github.io", "type": [ "Helpdesk" ], "note": "OmicsSuite Website" }, { "url": "https://space.bilibili.com/34105515", "type": [ "Social media" ], "note": "OmicsSuite Courses" }, { "url": "https://doi.org/10.1093/hr/uhad195", "type": [ "Helpdesk" ], "note": "OmicsSuite Paper" } ], "download": [ { "url": "https://omicssuite.github.io", "type": "Downloads page", "note": "GitHub download page", "version": "1.4.0" }, { "url": "https://sourceforge.net/projects/omicssuite-github-io/files/latest/download", "type": "Binaries", "note": "SourceForge download", "version": "1.4.0" }, { "url": "https://www.aliyundrive.com/s/Defuhf7FVGw", "type": "Binaries", "note": "ALiYun Drive", "version": "1.4.0" } ], "documentation": [], "publication": [ { "doi": "10.1093/hr/uhad195", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": "1.4.0", "note": "Ben-ben Miao, Wei Dong, Yi-xin Gu, Zhao-fang Han, Xuan Luo, Cai-huan Ke, Wei-wei You, OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data, Horticulture Research, 2023;, uhad195, https://doi.org/10.1093/hr/uhad195.", "metadata": { "title": "OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data", "abstract": "With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems; however, it is challenging for most experimental biologists to analyse data using command-line interfaces, coding, and scripting. Based on experience with multi-omics, we have developed OmicsSuite, a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization. The suite has 175 sub-applications in 12 categories, including Sequence, Statistics, Algorithm, Genomics, Transcriptomics, Enrichment, Proteomics, Metabolomics, Clinical, Microorganism, Single Cell, and Table Operation. We created the user interface with Sequence View, Table View, and intelligent components based on JavaFX and the popular Shiny framework. The multi-omics analysis functions were developed based on BioJava and 300+ packages provided by the R CRAN and Bioconductor communities, and it encompasses over 3000 adjustable parameter interfaces. OmicsSuite can directly read multi-omics raw data in FastA, FastQ, Mutation Annotation Format, mzML, Matrix, and HDF5 formats, and the programs emphasize data transfer directions and pipeline analysis functions. OmicsSuite can produce pre-publication images and tables, allowing users to focus on biological aspects. OmicsSuite offers multi-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in plants. It enables researchers to freely explore the molecular information contained in multi-omics big data (Source: https://github.com/OmicsSuite/, Website: https://omicssuite.github.io, v1.3.9).", "date": "2023-11-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Miao B.-B." }, { "name": "Dong W." }, { "name": "Gu Y.-X." }, { "name": "Han Z.-F." }, { "name": "Luo X." }, { "name": "Ke C.-H." }, { "name": "You W.-W." } ], "journal": "Horticulture Research" } } ], "credit": [], "community": null, "owner": "benben.miao", "additionDate": "2023-03-05T10:26:21.069202Z", "lastUpdate": "2024-02-25T14:20:44.230314Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Kaiju", "description": "Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses.", "homepage": "http://kaiju.binf.ku.dk", "biotoolsID": "kaiju", "biotoolsCURIE": "biotools:kaiju", "version": [ "1.4.4" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2975", "term": "Nucleic acid sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "Raw high-throughput sequencing reads (e.g. Illumina, Roche 454)", "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bioinformatics-centre/kaiju", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/bioinformatics-centre/kaiju", "type": "Source code", "note": null, "version": null }, { "url": "https://github.com/bioinformatics-centre/kaiju/releases/download/v1.4.4/kaiju-1.4.4-linux-x86_64.tar.gz", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://kaiju.binf.ku.dk", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/ncomms11257", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Fast and sensitive taxonomic classification for metagenomics with Kaiju", "abstract": "Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows-Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk.", "date": "2016-04-13T00:00:00Z", "citationCount": 491, "authors": [ { "name": "Menzel P." }, { "name": "Ng K.L." }, { "name": "Krogh A." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Peter Menzel", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Anders Krogh", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kim Lee Ng", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Section for Bioinformatics, Department of Biology, University of Copenhagen", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Elixir", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "binf.ku.dk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Peter Menzel", "email": "pmenzel@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Anders Krogh", "email": "krogh@binf.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "ptr@binf.ku.dk", "additionDate": "2016-10-19T14:56:00Z", "lastUpdate": "2024-02-21T13:53:35.628352Z", "editPermission": { "type": "group", "authors": [ "wenzel@sund.ku.dk" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Comet", "description": "Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool.", "homepage": "http://comet-ms.sourceforge.net/", "biotoolsID": "comet", "biotoolsCURIE": "biotools:comet", "version": [ "2016.01.2", "2023.01.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3646", "term": "Peptide database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrometry spectra" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3654", "term": "mzXML" }, { "uri": "http://edamontology.org/format_3651", "term": "MGF" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_3655", "term": "pepXML" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "C++" ], "license": "Apache-2.0", "collectionID": [ "Proteomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://sourceforge.net/projects/comet-ms/files/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://sourceforge.net/projects/comet-ms/files/", "type": "Source code", "note": null, "version": null }, { "url": "https://sourceforge.net/projects/comet-ms/files/", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://comet-ms.sourceforge.net/release/", "type": [ "Terms of use" ], "note": null }, { "url": "http://comet-ms.sourceforge.net/", "type": [ "Citation instructions", "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.201200439", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Comet: An open-source MS/MS sequence database search tool", "abstract": "Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.", "date": "2013-01-01T00:00:00Z", "citationCount": 891, "authors": [ { "name": "Eng J.K." }, { "name": "Jahan T.A." }, { "name": "Hoopmann M.R." } ], "journal": "Proteomics" } }, { "doi": "10.1007/s13361-015-1179-x", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "A Deeper Look into Comet - Implementation and Features", "abstract": "The Comet database search software was initially released as an open source project in late 2012. Prior to that, Comet existed as the University of Washington's academic version of the SEQUEST database search tool. Despite its availability and widespread use over the years, some details about its implementation have not been previously disseminated or are not well understood. We address a few of these details in depth and highlight new features available in the latest release. Comet is freely available for download at http://comet-ms.sourceforge.net or it can be accessed as a component of a number of larger software projects into which it has been incorporated. (Figure Presented).", "date": "2015-11-01T00:00:00Z", "citationCount": 131, "authors": [ { "name": "Eng J.K." }, { "name": "Hoopmann M.R." }, { "name": "Jahan T.A." }, { "name": "Egertson J.D." }, { "name": "Noble W.S." }, { "name": "MacCoss M.J." } ], "journal": "Journal of the American Society for Mass Spectrometry" } } ], "credit": [ { "name": "lumc.nl", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Comet's Google group", "email": null, "url": "https://groups.google.com/forum/#!forum/comet-ms", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "Comet's Google group", "email": null, "url": "https://groups.google.com/forum/#!forum/comet-ms", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "admin", "additionDate": "2016-04-12T11:22:47Z", "lastUpdate": "2024-02-16T12:32:41.278020Z", "editPermission": { "type": "group", "authors": [ "n.m.palmblad@lumc.nl", "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "compareMS2", "description": "compareMS2 is a tool for comparing sets of (tandem) mass spectra for clustering samples, molecular phylogenetics, identification of biological species or tissues, and quality control. compareMS2 currently consumes Mascot Generic Format, or MGF, and produces output in a variety of common image and distance matrix formats.", "homepage": "https://github.com/524D/compareMS2", "biotoolsID": "comparems2", "biotoolsCURIE": "biotools:comparems2", "version": [ "1.0", "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2424", "term": "Comparison" }, { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3651", "term": "MGF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3272", "term": "Species tree" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_2855", "term": "Distance matrix" }, "format": [ { "uri": "http://edamontology.org/format_1991", "term": "mega" }, { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C", "JavaScript" ], "license": "MIT", "collectionID": [ "ms-utils", "Proteomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Netherlands" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/524D/compareMS2", "type": [ "Repository" ], "note": null }, { "url": "https://www.ms-utils.org/compareMS2.html", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.ms-utils.org/compareMS2.c", "type": "Source code", "note": null, "version": "1.0" }, { "url": "http://www.ms-utils.org/compareMS2.html", "type": "Binaries", "note": null, "version": "1.0" }, { "url": "http://www.ms-utils.org/compareMS2.c", "type": "Source code", "note": null, "version": "1.0" }, { "url": "https://github.com/524D/compareMS2/tree/main/src", "type": "Source code", "note": null, "version": "2.0" }, { "url": "https://github.com/524D/compareMS2/tree/main", "type": "Binaries", "note": null, "version": "2.0" } ], "documentation": [ { "url": "http://www.ms-utils.org/compareMS2.html", "type": [ "General", "Command-line options" ], "note": null }, { "url": "https://github.com/524D/compareMS2", "type": [ "General", "User manual", "Command-line options", "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1002/rcm.6162", "pmid": "22368051", "pmcid": null, "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "Molecular phylogenetics by direct comparison of tandem mass spectra", "abstract": "Rationale: Molecular phylogenetics is the study of evolution and relatedness of organisms or genes. Mass spectrometry is used routinely for bacterial identification and has also been used for phylogenetic analysis, for instance from bone material. Unfortunately, only a small fraction of the acquired tandem mass spectra allow direct interpretation. Methods: We describe a new algorithm and software for molecular phylogenetics using pairwise comparisons of tandem mass spectra from enzymatically digested proteins. The spectra need not be annotated and all acquired data is used in the analysis. To demonstrate the method, we analyzed tryptic digests of sera from four great apes and two other primates. Results: The distribution of spectra dot products for thousands of tandem mass spectra collected from two samples provides a measure on the fraction of shared peptides between the two samples. When inverted, this becomes a distance metric. By pairwise comparison between species and averaging over four individuals per species, it was possible to reconstruct the unique correct phylogenetic tree for the great apes and other primates. Conclusions: The new method described here has several attractive features compared with existing methods, among them simplicity, the unbiased use of all acquired data rather than a small subset of spectra, and the potential use of heavily degraded proteins or proteins with a priori unknown modifications. © 2012 John Wiley & Sons, Ltd.", "date": "2012-04-15T00:00:00Z", "citationCount": 28, "authors": [ { "name": "Palmblad M." }, { "name": "Deelder A.M." } ], "journal": "Rapid Communications in Mass Spectrometry" } }, { "doi": "10.1021/acs.jproteome.2c00457", "pmid": "36173614", "pmcid": "PMC9903320", "type": [ "Other" ], "version": "2.0", "note": null, "metadata": { "title": "compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets", "abstract": "It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected in proteomics. This method has seen use in species identification and mixture characterization in food and feed products, as well as other applications. Here, we present the first major update of this software, including a new metric, a graphical user interface and additional functionality. The data have been deposited to ProteomeXchange with dataset identifier PXD034932.", "date": "2023-02-03T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Marissen R." }, { "name": "Varunjikar M.S." }, { "name": "Laros J.F.J." }, { "name": "Rasinger J.D." }, { "name": "Neely B.A." }, { "name": "Palmblad M." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.1c00528", "pmid": "34523928", "pmcid": "PMC8491155", "type": [ "Review" ], "version": "2.0", "note": null, "metadata": { "title": "Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics", "abstract": "Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics. In the decades following, proteins continued to provide essential clues on evolutionary history. While technology has continued to improve, contemporary proteomics has strayed from this larger biological context, rarely comparing species or asking how protein structure, function, and interactions have evolved. Here we recombine proteomics with molecular phylogenetics, highlighting the value of framing proteomic results in a larger biological context and how almost forgotten research, though technologically surpassed, can still generate new ideas and illuminate our work from a different perspective. Though it is infeasible to read all research published on a large topic, looking up older papers can be surprisingly rewarding when rediscovering a \"gem\"at the end of a long citation chain, aided by digital collections and perpetually helpful librarians. Proper literature study reduces unnecessary repetition and allows research to be more insightful and impactful by truly standing on the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/) as dataset MSV000087993.", "date": "2021-10-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Neely B.A." }, { "name": "Palmblad M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "lumc.nl", "email": null, "url": "https://www.lumc.nl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Support" ], "note": null }, { "name": "Magnus Palmblad", "email": "magnus.palmblad@gmail.com", "url": "https://github.com/magnuspalmblad", "orcidid": "http://orcid.org/0000-0002-5865-8994", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Documentor" ], "note": null }, { "name": "Rob Marissen", "email": null, "url": "https://github.com/524D", "orcidid": "https://orcid.org/0000-0002-1220-9173", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "community": null, "owner": "n.m.palmblad@lumc.nl", "additionDate": "2016-04-15T11:52:42Z", "lastUpdate": "2024-02-13T15:35:10.776331Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Jalview", "description": "Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.", "homepage": "https://www.jalview.org/", "biotoolsID": "Jalview", "biotoolsCURIE": "biotools:Jalview", "version": [ "2.11.3.2" ], "otherID": [], "relation": [ { "biotoolsID": "jabaws", "type": "uses" }, { "biotoolsID": "chimera", "type": "uses" }, { "biotoolsID": "chimerax", "type": "uses" }, { "biotoolsID": "pymol", "type": "uses" }, { "biotoolsID": "bioconda", "type": "includedIn" }, { "biotoolsID": "3d-beacons", "type": "uses" }, { "biotoolsID": "uniprot", "type": "uses" }, { "biotoolsID": "pfam", "type": "uses" }, { "biotoolsID": "ensembl", "type": "uses" }, { "biotoolsID": "pdb", "type": "uses" }, { "biotoolsID": "rfam", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_0324", 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"Executable JAR file", "version": null } ], "documentation": [ { "url": "https://www.jalview.org/about/citation", "type": [ "Citation instructions" ], "note": null }, { "url": "https://www.jalview.org/training/", "type": [ "Training material" ], "note": "Hands-on exercises, Training courses and Training videos" }, { "url": "https://www.jalview.org/help/faq", "type": [ "FAQ" ], "note": null }, { "url": "https://www.jalview.org/help/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp033", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Jalview Version 2-A multiple sequence alignment editor and analysis workbench", "abstract": "Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. © 2009 The Author(s).", "date": "2009-05-07T00:00:00Z", "citationCount": 6231, "authors": [ { "name": "Waterhouse A.M." }, { "name": "Procter J.B." }, { "name": "Martin D.M.A." }, { "name": "Clamp M." }, { "name": "Barton G.J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Jim Procter", "email": null, "url": "http://www.lifesci.dundee.ac.uk/people/jim-procter", "orcidid": "https://orcid.org/0000-0002-7865-7382", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Geoff Barton", "email": null, "url": "https://www.lifesci.dundee.ac.uk/people/geoff-barton", "orcidid": "https://orcid.org/0000-0002-9014-5355", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "ben_s", "additionDate": "2019-02-13T17:01:40Z", "lastUpdate": "2023-12-01T12:00:21.286261Z", "editPermission": { "type": "group", "authors": [ "ben_s", "jimprocter" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PIA - Protein Inference Algorithms", "description": "The main focus lays on the integrated inference algorithms, concluding the proteins from a set of identified spectra. But it also allows you to integrate results of various search engines, inspect your peptide spectrum matches, calculate FDR values across different results and visualize the correspondence between PSMs, peptides and proteins.", "homepage": "https://github.com/medbioinf/pia", "biotoolsID": "pia", "biotoolsCURIE": "biotools:pia", "version": [ "1.4" ], "otherID": [], "relation": [ { "biotoolsID": "knime", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrometry spectra" }, "format": [ { "uri": "http://edamontology.org/format_3713", "term": "Mascot .dat file" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3684", "term": "PRIDE XML" }, { "uri": "http://edamontology.org/format_3711", "term": "X!Tandem XML" }, { "uri": "http://edamontology.org/format_3702", "term": "MSF" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" }, { "uri": "http://edamontology.org/format_3765", "term": "KNIME datatable format" }, { "uri": "http://edamontology.org/format_3764", "term": "idXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" } ] }, { "data": { "uri": "http://edamontology.org/data_0989", "term": "Protein identifier" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" }, { "uri": "http://edamontology.org/format_3765", "term": "KNIME datatable format" }, { "uri": "http://edamontology.org/format_3764", "term": "idXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" } ] } ], "note": "PIA allows you to inspect the results of common proteomics spectrum identification search engines, combine them seamlessly and conduct statistical analyses. The main focus of PIA lays on the integrated inference algorithms, i.e. concluding the proteins from a set of identified spectra. But it also allows you to inspect your peptide spectrum matches, calculate FDR values across different search engine results and visualize the correspondence between PSMs, peptides and proteins. Search engine results in several formats peptide spectrum matches (PSMs) and peptides Inferred Proteins", "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Desktop application", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3120", "term": "Protein variants" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "BSD-3-Clause", "collectionID": [ "KNIME", "de.NBI", "Proteomics", "BioInfra.Prot", "CUBiMed.RUB" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/medbioinf/pia", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/mpc-bioinformatics/pia", "type": "Source code", "note": null, "version": null }, { "url": "http://bioconda.github.io/recipes/pia/README.html", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/mpc-bioinformatics/pia/releases", "type": "Binaries", "note": null, "version": null }, { "url": "https://hub.docker.com/r/julianusz/pia", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/mpc-bioinformatics/pia/wiki", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.5b00121", "pmid": "25938255", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface", "abstract": "Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.", "date": "2015-07-02T00:00:00Z", "citationCount": 53, "authors": [ { "name": "Uszkoreit J." }, { "name": "Maerkens A." }, { "name": "Perez-Riverol Y." }, { "name": "Meyer H.E." }, { "name": "Marcus K." }, { "name": "Stephan C." }, { "name": "Kohlbacher O." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.8b00723", "pmid": "30474983", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Protein Inference Using PIA Workflows and PSI Standard File Formats", "abstract": "Proteomics using LC-MS/MS has become one of the main methods to analyze the proteins in biological samples in high-throughput. But the existing mass-spectrometry instruments are still limited with respect to resolution and measurable mass ranges, which is one of the main reasons why shotgun proteomics is the major approach. Here proteins are digested, which leads to the identification and quantification of peptides instead. While often neglected, the important step of protein inference needs to be conducted to infer from the identified peptides to the actual proteins in the original sample. In this work, we highlight some of the previously published and newly added features of the tool PIA - Protein Inference Algorithms, which helps the user with the protein inference of measured samples. We also highlight the importance of the usage of PSI standard file formats, as PIA is the only current software supporting all available standards used for spectrum identification and protein inference. Additionally, we briefly describe the benefits of working with workflow environments for proteomics analyses and show the new features of the PIA nodes for the KNIME Analytics Platform. Finally, we benchmark PIA against a recently published data set for isoform detection. PIA is open source and available for download on GitHub (https://github.com/mpc-bioinformatics/pia) or directly via the community extensions inside the KNIME analytics platform.", "date": "2019-02-01T00:00:00Z", "citationCount": 25, "authors": [ { "name": "Uszkoreit J." }, { "name": "Perez-Riverol Y." }, { "name": "Eggers B." }, { "name": "Marcus K." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "Julian Uszkoreit", "email": "julian.uszkoreit@rub.de", "url": null, "orcidid": "http://orcid.org/0000-0001-7522-4007", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "CUBiMed.RUB", "email": "cubimed@rub.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "community": null, "owner": "julianu", "additionDate": "2016-07-12T10:54:05Z", "lastUpdate": "2023-11-29T13:17:14.978741Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AtomicChargeCalculator", "description": "A web application for the calculation and analysis of atomic charges in both large biomolecular complexes and small drug-like molecules.", "homepage": "https://ncbr.muni.cz/ACC", "biotoolsID": "atomicchargecalculator", "biotoolsCURIE": "biotools:atomicchargecalculator", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_2480", "term": "Structure analysis" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2085", "term": "Structure report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_1917", "term": "Atomic property" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C#" ], "license": null, "collectionID": [ "LCC NCBR", "Czech Republic", "ELIXIR-CZ", "CEITEC" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [ { "url": "https://webchemdev.ncbr.muni.cz/Platform/ChargeCalculator", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://webchem.ncbr.muni.cz/Platform/ChargeCalculator/DownloadService", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://www.jcheminf.com/content/7/1/50/citation", "type": [ "Citation instructions" ], "note": null }, { "url": "http://webchem.ncbr.muni.cz/Wiki/ChargeCalculator:UserManual", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s13321-015-0099-x", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "AtomicChargeCalculator: Interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules", "abstract": "Background: Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites. Results: This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form. Conclusions: Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC.", "date": "2015-10-22T00:00:00Z", "citationCount": 50, "authors": [ { "name": "Ionescu C.-M." }, { "name": "Sehnal D." }, { "name": "Falginella F.L." }, { "name": "Pant P." }, { "name": "Pravda L." }, { "name": "Bouchal T." }, { "name": "Svobodova Varekova R." }, { "name": "Geidl S." }, { "name": "Koca J." } ], "journal": "Journal of Cheminformatics" } } ], "credit": [ { "name": "David Sehnal", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Crina Maria Ionescu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Stanislav Geidl", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Lukáš Pravda", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Masaryk University, Brno, Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Primary Contact", "email": "webchemistryhelp@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "David Sehnal", "email": "david.sehnal@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Maintainer" ], "note": null }, { "name": "Crina Maria Ionescu", "email": "crina_i@hotmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "Primary Contact", "email": "webchemistryhelp@gmail.com", "url": "https://webchem.ncbr.muni.cz", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "David Sehnal", "email": "david.sehnal@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Crina Maria Ionescu", "email": "crina_i@hotmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "ELIXIR-CZ", "additionDate": "2015-12-01T18:10:32Z", "lastUpdate": "2023-11-27T09:19:15.101428Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }
