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"confidence_flag": null }, { "name": "RhizoVision Explorer", "description": "RhizoVision Explorer is free and open-source software developed for estimating root traits from images acquired from a flatbed scanner or camera. Root images are expected to have a high contrast of roots with the background, homogenous lighting, and minimal overlapping of roots.", "homepage": "https://github.com/noble-research-institute/RhizoVisionExplorer", "biotoolsID": "rhizovision-explorer", "biotoolsCURIE": "biotools:rhizovision-explorer", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3937", "term": "Feature extraction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_3298", "term": "Phenomics" } ], "operatingSystem": [], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/rootphenomicslab/RhizoVisionExplorer/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/aobpla/plab056", "pmid": "34804466", "pmcid": "PMC8598384", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "RhizoVision Explorer: Open-source software for root image analysis and measurement standardization", "abstract": "Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software designed to enable researchers interested in roots by providing an easy-To-use interface, fast image processing and reliable measurements. The default broken roots mode is intended for roots sampled from pots and soil cores, washed and typically scanned on a flatbed scanner, and provides measurements like length, diameter and volume. The optional whole root mode for complete root systems or root crowns provides additional measurements such as angles, root depth and convex hull. Both modes support providing measurements grouped by defined diameter ranges, the inclusion of multiple regions of interest and batch analysis. RhizoVision Explorer was successfully validated against ground truth data using a new copper wire image set. In comparison, the current reference software, the commercial WinRhizo™, drastically underestimated volume when wires of different diameters were in the same image. Additionally, measurements were compared with WinRhizo™ and IJ_Rhizo using a simulated root image set, showing general agreement in software measurements, except for root volume. Finally, scanned root image sets acquired in different labs for the crop, herbaceous and tree species were used to compare results from RhizoVision Explorer with WinRhizo™. The two software showed general agreement, except that WinRhizo™ substantially underestimated root volume relative to RhizoVision Explorer. In the current context of rapidly growing interest in root science, RhizoVision Explorer intends to become a reference software, improve the overall accuracy and replicability of root trait measurements and provide a foundation for collaborative improvement and reliable access to all.", "date": "2021-12-01T00:00:00Z", "citationCount": 130, "authors": [ { "name": "Seethepalli A." }, { "name": "Dhakal K." }, { "name": "Griffiths M." }, { "name": "Guo H." }, { "name": "Freschet G.T." }, { "name": "York L.M." } ], "journal": "AoB PLANTS" } } ], "credit": [ { "name": "Larry M. York", "email": "lmyork@noble.org", "url": null, "orcidid": "https://orcid.org/0000-0002-1995-9479", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-11-29T10:31:42.544157Z", "lastUpdate": "2026-03-17T09:34:03.454691Z", "editPermission": { "type": "group", "authors": [ "RDKing" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Freezing-Point", "description": "Freezing-Point is a user-friendly open-source software for the automated analysis of freezing behavior in rodents. Based on recorded videos or pose estimation files. An adaptive, data-driven algorithm automatically determines freezing detection thresholds, reducing subjective bias while preserving user oversight. Freezing-Point adopts a user-oriented design centered on a graphical interface that provides continuous visual access to original data, processing steps and analysis results. 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Computes normal modes, fluctuation profiles, inter-residue correlations, conformational overlap analysis and vector field representations. Structural amino acid profiles, and normal mode characteristics describing protein motion, visualized in plots and decorated structure visualizations. White space delimited tabular data for normal modes and the provided plots", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2487", "term": "Protein structure comparison" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0886", "term": "Structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_0889", "term": "Structural profile" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Performs comparative analysis of the normal modes of protein structures. Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins to be compared. Multiple protein structures Heatmaps, dendrograms and structural amino acid profiles for visual comparison of structural similarity. White space delimited tabular data for the provided plots", "cmd": null } ], "toolType": [ "Web API", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "BiB tools", "CBU tools", "UiB tools", "ELIXIR-NO", "ELIXIR-Norway" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Norway" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://github.com/reuter-group/webnma3", "type": [ "Repository", "Issue tracker" ], "note": null }, { "url": "https://elixir.no/helpdesk", "type": [ "Helpdesk" ], "note": "Helpdesk and support for ELIXIR Norway services." } ], "download": [], "documentation": [ { "url": "http://apps.cbu.uib.no/webnma3/howto/single", "type": [ "Quick start guide" ], "note": null }, { "url": "http://apps.cbu.uib.no/webnma3/qanda", "type": [ "FAQ" ], "note": null }, { "url": "http://apps.cbu.uib.no/webnma3/about", "type": [ "General", "Citation instructions" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-014-0427-6", "pmid": "25547242", "pmcid": "PMC4339738", "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "WEBnmat v2.0: Web server and services for comparing protein flexibility", "abstract": "Background: Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. Results: We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnmat, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the. In addition, programmatic access to WEBnmat is now available through a SOAP-based web service. WEBnmat is available at. Conclusion: WEBnmat v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnmat facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.", "date": "2014-12-30T00:00:00Z", "citationCount": 87, "authors": [ { "name": "Tiwari S.P." }, { "name": "Fuglebakk E." }, { "name": "Hollup S.M." }, { "name": "Skjaerven L." }, { "name": "Cragnolini T." }, { "name": "Grindhaug S.H." }, { "name": "Tekle K.M." }, { "name": "Reuter N." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1186/1471-2105-6-52", "pmid": "15762993", "pmcid": "PMC1274249", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "WEBnm@: A web application for normal mode analyses of proteins", "abstract": "Background: Normal mode analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. NMA is especially useful for large biomolecular assemblies, such as transmembrane channels or virus capsids. NMA relies on the hypothesis that the vibrational normal modes having the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones that are functionally relevant. Results: We developed a web-based server to perform normal modes calculations and different types of analyses. Starting from a structure file provided by the user in the PDB format, the server calculates the normal modes and subsequently offers the user a series of automated calculations; normalized squared atomic displacements, vector field representation and animation of the first six vibrational modes. Each analysis is performed independently from the others and results can be visualized using only a web browser. No additional plug-in or software is required. For users who would like to analyze the results with their favorite software, raw results can also be downloaded. The application is available on http://www.bioinfo.no/tools/normalmodes. We present here the underlying theory, the application architecture and an illustration of its features using a large transmembrane protein as an example. Conclusion: We built an efficient and modular web application for normal mode analysis of proteins. Non specialists can easily and rapidly evaluate the degree of flexibility of multi-domain protein assemblies and characterize the large amplitude movements of their domains. © 2005 Hollup et al; licensee BioMed Central Ltd.", "date": "2005-03-11T00:00:00Z", "citationCount": 105, "authors": [ { "name": "Hollup S.M." }, { "name": "Salensminde G." }, { "name": "Reuter N." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Nathalie Reuter", "email": "Nathalie.Reuter@uib.no", "url": "http://www.cbu.uib.no/reuter/", "orcidid": "https://orcid.org/0000-0002-3649-7675", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Sandhya P Tiwari", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-0747-3826", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kidane M Tekle", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Tristan Cragnolini", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Svenn H Grindhaug", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Lars Skjærven", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Gisle Salensminde", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Edvin Fuglebakk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Siv M Hollup", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Department of Molecular Biology, University of Bergen, Norway", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Computational Biology Unit, Department of Informatics, University of Bergen, Norway", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "UiB", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "UiB", "additionDate": "2016-03-17T13:51:10Z", "lastUpdate": "2026-03-11T08:56:55.566213Z", "editPermission": { "type": "group", "authors": [ "eca008", "korbinib" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioMercator", "description": "BioMercator is a software that provides a complete set of algorithms and visualization tool covering all steps required to perform QTL meta-analysis, graphical representation of large datasets. User may import sequence and genome annotations datasets within the software in order to display functional annotation related to QTL and meta-QTL.", "homepage": "https://sourcesup.renater.fr/projects/biomercator", "biotoolsID": "BioMercator", "biotoolsCURIE": "biotools:BioMercator", "version": [ "4.2.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0282", "term": "Genetic mapping" }, { "uri": "http://edamontology.org/operation_2944", "term": "Physical mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1860", "term": "QTL map" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1288", "term": "Genome map" }, "format": [ { "uri": "http://edamontology.org/format_1975", "term": "GFF3" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3055", "term": "Quantitative genetics" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://sourcesup.renater.fr/frs/?group_id=2301", "type": "Binaries", "note": null, "version": "4.2.3" } ], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/bth230", "pmid": "15059820", "pmcid": null, "type": [], "version": "3", "note": null, "metadata": { "title": "BioMercator: Integrating genetic maps and QTL towards discovery of candidate genes", "abstract": "Summary: Breeding programs face the challenge of integrating information from genomics and from quantitative trait loci (QTL) analysis in order to identify genomic sequences controlling the variation of important traits. Despite the development of integrative databases, building a consensus map of genes, QTL and other loci gathered from multiple maps remains a manual and tedious task. Nevertheless, this is a critical step to reveal co-locations between genes and QTL. Another important matter is to determine whether QTL linked to same traits or related ones is detected in independent experiments and located in the same region, and represents a single locus or not. Statistical tools such as meta-analysis can be used to answer this question. BioMercator has been developed to automate map compilation and QTL meta-analysis, and to visualize co-locations between genes and QTL through a graphical interface. © Oxford University Press 2004; all rights reserved.", "date": "2004-09-22T00:00:00Z", "citationCount": 382, "authors": [ { "name": "Arcade A." }, { "name": "Labourdette A." }, { "name": "Falque M." }, { "name": "Mangin B." }, { "name": "Chardon F." }, { "name": "Charcosset A." }, { "name": "Joets J." } ], "journal": "Bioinformatics" } } ], "credit": [], "owner": "admin", "additionDate": "2019-09-27T09:58:46Z", "lastUpdate": "2026-03-11T08:56:54.859634Z", "editPermission": { "type": "group", "authors": [ "b.guerra01" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BigSeqKit", "description": "The Next Generation Sequencing (NGS) raw data are stored in FASTA and FASTQ text-based file formats. Common operations on FASTA/Q files include searching, filtering, sampling, deduplication and sorting, among others. We can find several tools in the literature for FASTA/Q file manipulation but none of them are well fitted for large files of tens of GB (likely TBs in the near future) since mostly they are based on sequential processing. The exception is seqkit that allows some routines to use a few threads but, in any case, the scalability is very limited. To deal with this issue, we introduce BigSeqKit, a parallel toolkit to manipulate FASTA/Q files at scale with speed and scalability at its core. BigSeqKit takes advantage of an HPC-Big Data framework (IgnisHPC) to parallelize and optimize the commands included in seqkit. In this way, in most cases it is from tens to hundreds of times faster than other state-of-the-art tools such as seqkit, samtools and pyfastx.", "homepage": "https://github.com/citiususc/BigSeqKit", "biotoolsID": "bigseqkit", "biotoolsCURIE": "biotools:bigseqkit", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" }, { "uri": "http://edamontology.org/operation_0372", "term": "DNA transcription" }, { "uri": "http://edamontology.org/operation_0371", "term": "DNA translation" }, { "uri": "http://edamontology.org/operation_0233", "term": "Sequence conversion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "cesarpomar", "additionDate": "2023-05-22T15:10:32.141196Z", "lastUpdate": "2026-03-01T11:28:15.208151Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PLAST", "description": "PLAST is a heuristical method to search for highest scoring local alignments between a DNA sequence query and a graphical pangenome. It takes as input a plain DNA sequence and a pangenome which may either be a set of (multiple) FASTA or FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard output format. Alignments are calculated based on a \"seed-and-extend approach\" while traversing the sequence graph. Biologically meaningful alignments are filtered by using an alignment statistic explicitly developed for sequence-to-graph alignments involving graphical pangenomes.", "homepage": "https://github.com/tischulz1/plast", "biotoolsID": "pangenome-blast", "biotoolsCURIE": "biotools:pangenome-blast", "version": [ "0.0.1-0.2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1211", "term": "unambiguous pure nucleotide" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_3975", "term": "GFA 1" }, { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1333", "term": "BLAST results" } ] } ], "note": "In order to search for alignments within the pangenome graph, \nA pangenome graph used to search for alignments consists of (1) a file in GFA format containing all sequences of the graph, (2) a binary file produced by the tool itself or the software \"Bifrost\" and (3) a program-specific index data structure in binary format.", "cmd": "PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLine" }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_3975", "term": "GFA 1" }, { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "note": "If a pangenome graph already exists and only an index has to be built, FASTA/FASTQ files are not needed.", "cmd": "PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fasta" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.ub.uni-bielefeld.de/gi/plast", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/tischulz1/plast", "type": [ "Mirror" ], "note": null } ], "download": [], "documentation": [ { "url": "https://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btab077", "pmid": "33532821", "pmcid": "PMC8388040", "type": [ "Primary", "Method", "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Detecting high-scoring local alignments in pangenome graphs", "abstract": "Motivation: Increasing amounts of individual genomes sequenced per species motivate the usage of pangenomic approaches. Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet. Results: We present a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. Our approach additionally allows a comparison of similarity among sequences within the pangenome. We show that local alignment scores follow an exponential-tail distribution similar to BLAST scores, and we discuss how to estimate its parameters to separate local alignments representing sequence homology from spurious findings. An implementation of our method is presented, and its performance and usability are shown. Our approach scales sublinearly in running time and memory usage with respect to the number of genomes under consideration. This is an advantage over classical methods that do not make use of sequence similarity within the pangenome.", "date": "2021-08-15T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Schulz T." }, { "name": "Wittler R." }, { "name": "Rahmann S." }, { "name": "Hach F." }, { "name": "Stoye J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Bielefeld University", "email": null, "url": "https://www.uni-bielefeld.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Genome Informatics", "email": null, "url": "https://gi.cebitec.uni-bielefeld.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Tizian Schulz", "email": "plast-service@cebitec.uni-bielefeld.de", "url": null, "orcidid": "https://orcid.org/0000-0003-0744-7078", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "tizian", "additionDate": "2021-05-06T06:18:52Z", "lastUpdate": "2026-02-26T11:22:02.485629Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ESIprot", "description": "Charge state determination and molecular weight calculation for low resolution electrospray ionization data.", "homepage": "https://nube-gran.de/esiprot", "biotoolsID": "esiprot", "biotoolsCURIE": "biotools:esiprot", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0398", "term": "Protein molecular weight calculation" }, { "uri": "http://edamontology.org/operation_2929", "term": "Protein fragment weight comparison" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0944", "term": "Peptide mass fingerprint" }, "format": [ { "uri": "http://edamontology.org/format_3245", "term": "Mass spectrometry data format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0944", "term": "Peptide mass fingerprint" }, "format": [ { "uri": "http://edamontology.org/format_3245", "term": "Mass spectrometry data format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.bioprocess.org/esiprot/esiprot_form.php", "type": [ "Mirror" ], "note": null }, { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.bioprocess.org/esiprot/esiprot.zip", "type": "Source code", "note": null, "version": null }, { "url": "http://www.bioprocess.org/esiprot/esiprot.zip", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://www.lababi.bioprocess.org/index.php/lababi-software/84-esiprot", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/rcm.4384", "pmid": "20049890", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ESIprot: A universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data", "abstract": "Electrospray ionization (ESI) ion trap mass spectrometers with relatively low resolution are frequently used for the analysis of natural products and peptides. Although ESI spectra of multiply charged protein molecules also can be measured on this type of devices, only average spectra are produced for the majority of naturally occurring proteins. Evaluating such ESI protein spectra would provide valuable information about the native state of investigated proteins. However, no suitable and freely available software could be found which allows the charge state determination and molecular weight calculation of single proteins from average ESI-MS data. Therefore, an algorithm based on standard deviation optimization (scatter minimization) was implemented for the analysis of protein ESI-MS data. The resulting software ESIprot was tested with ESI-MS data of six intact reference proteins between 12.4 and 66.7kDa. In all cases, the correct charge states could be determined. The obtained absolute mass errors were in a range between -0.2 and 1.2Da, the relative errors below 30ppm. The possible mass accuracy allows for valid conclusions about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates an extraordinary robustness and allows spectral interpretation from as little as two peaks, given sufficient quality of the provided m/z data, without the necessity for peak intensity data. ESIprot is independent from the raw data format and the computer platform, making it a versatile tool for mass spectrometrists. 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