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{ "count": 215, "next": "?page=2", "previous": null, "list": [ { "name": "ntLink", "description": "Toolkit for de novo genome assembly scaffolding and mapping using long reads.", "homepage": "https://github.com/bcgsc/ntLink", "biotoolsID": "ntlink", "biotoolsCURIE": "biotools:ntlink", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3216", "term": "Scaffolding" }, { "uri": "http://edamontology.org/operation_0524", "term": "De-novo assembly" }, { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" }, { "uri": "http://edamontology.org/operation_0523", "term": "Mapping assembly" }, { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bcgsc/ntLink.git", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1002/CPZ1.733", "pmid": "37039735", "pmcid": "PMC10091225", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads", "abstract": "With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the generation of high-quality genome assemblies in a computationally efficient manner are essential. Recent developments in long-read sequencing technologies have greatly benefited genome assembly work, including scaffolding, by providing long-range evidence that can aid in resolving the challenging repetitive regions of complex genomes. ntLink is a flexible and resource-efficient genome scaffolding tool that utilizes long-read sequencing data to improve upon draft genome assemblies built from any sequencing technologies, including the same long reads. Instead of using read alignments to identify candidate joins, ntLink utilizes minimizer-based mappings to infer how input sequences should be ordered and oriented into scaffolds. Recent improvements to ntLink have added important features such as overlap detection, gap-filling, and in-code scaffolding iterations. Here, we present three basic protocols demonstrating how to use each of these new features to yield highly contiguous genome assemblies, while still maintaining ntLink's proven computational efficiency. Further, as we illustrate in the alternate protocols, the lightweight minimizer-based mappings that enable ntLink scaffolding can also be utilized for other downstream applications, such as misassembly detection. With its modularity and multiple modes of execution, ntLink has broad benefit to the genomics community, from genome scaffolding and beyond. ntLink is an open-source project and is freely available from https://github.com/bcgsc/ntLink. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: ntLink scaffolding using overlap detection. Basic Protocol 2: ntLink scaffolding with gap-filling. Basic Protocol 3: Running in-code iterations of ntLink scaffolding. Alternate Protocol 1: Generating long-read to contig mappings with ntLink. Alternate Protocol 2: Using ntLink mappings for genome assembly correction with Tigmint-long. Support Protocol: Installing ntLink.", "date": "2023-04-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Coombe L." }, { "name": "Warren R.L." }, { "name": "Wong J." }, { "name": "Nikolic V." }, { "name": "Birol I." } ], "journal": "Current Protocols" } } ], "credit": [ { "name": "Lauren Coombe", "email": "lcoombe@bcgsc.ca", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Inanc Birol", "email": "ibirol@bcgsc.ca", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-09-15T16:26:06.061484Z", "lastUpdate": "2023-09-15T16:26:06.064198Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "STAR", "description": "Ultrafast universal RNA-seq data aligner", "homepage": "http://code.google.com/p/rna-star/", "biotoolsID": "star", "biotoolsCURIE": "biotools:star", "version": [ "2.7.11" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] }, { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [ "Animal and Crop Genomics" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/alexdobin/STAR/releases", "type": [ "Release notes" ], "note": null }, { "url": "https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts635", "pmid": "23104886", "pmcid": "PMC3530905", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "STAR: Ultrafast universal RNA-seq aligner", "abstract": "Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases.Results: To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. © The Author(s) 2012. Published by Oxford University Press.", "date": "2013-01-01T00:00:00Z", "citationCount": 21778, "authors": [ { "name": "Dobin A." }, { "name": "Davis C.A." }, { "name": "Schlesinger F." }, { "name": "Drenkow J." }, { "name": "Zaleski C." }, { "name": "Jha S." }, { "name": "Batut P." }, { "name": "Chaisson M." }, { "name": "Gingeras T.R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1038/nmeth.4106", "pmid": "27941783", "pmcid": "PMC5792058", "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Simulation-based comprehensive benchmarking of RNA-seq aligners", "abstract": "Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. We performed a comprehensive benchmarking of 14 common splice-aware aligners for base, read, and exon junction-level accuracy and compared default with optimized parameters. We found that performance varied by genome complexity, and accuracy and popularity were poorly correlated. The most widely cited tool underperforms for most metrics, particularly when using default settings.", "date": "2017-02-01T00:00:00Z", "citationCount": 147, "authors": [ { "name": "Baruzzo G." }, { "name": "Hayer K.E." }, { "name": "Kim E.J." }, { "name": "DI Camillo B." }, { "name": "Fitzgerald G.A." }, { "name": "Grant G.R." } ], "journal": "Nature Methods" } }, { "doi": "10.1093/bioinformatics/btu146", "pmid": "24626854", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Lacking alignments? The next-generation sequencing mapper segemehl revisited", "abstract": "Motivation: Next-generation sequencing has become an important tool in molecular biology. Various protocols to investigate genomic, transcriptomic and epigenomic features across virtually all species and tissues have been devised. For most of these experiments, one of the first crucial steps of bioinformatic analysis is the mapping of reads to reference genomes. Results: Here, we present thorough benchmarks of our read aligner segemehl in comparison with other state-of-the-art methods. Furthermore, we introduce the tool lack to rescue unmapped RNA-seq reads which works in conjunction with segemehl and many other frequently used split-read aligners. © The Author 2014.", "date": "2014-07-01T00:00:00Z", "citationCount": 63, "authors": [ { "name": "Otto C." }, { "name": "Stadler P.F." }, { "name": "Hoffmann S." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "rna-styar team", "email": "dobin@cshl.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "seqwiki_import", "additionDate": "2017-01-13T13:16:43Z", "lastUpdate": "2023-08-31T03:31:28.075202Z", "editPermission": { "type": "group", "authors": [ "hmenager", "animalandcropgenomics", "billsfriend" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BRIDGEcereal", "description": "BRIDGEcereal provides a user-friendly interface to efficiently identify large indels from pan-genomes of major cereal crops, accelerating gene discovery for important traits.", "homepage": "https://bridgecereal.scinet.usda.gov", "biotoolsID": "bridgecereal", "biotoolsCURIE": "biotools:bridgecereal", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0452", "term": "Indel detection" }, { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_0487", "term": "Haplotype mapping" }, { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" }, { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0865", "term": "Sequence similarity score" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/xianranli/CHOICE_CLIPS", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://bridgecereal.scinet.usda.gov/Instruction", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1016/j.molp.2023.05.005", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Streamline unsupervised machine learning to survey and graph indel-based haplotypes from pan-genomes", "abstract": "", "date": "2023-06-05T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Zhang B." }, { "name": "Huang H." }, { "name": "Tibbs-Cortes L.E." }, { "name": "Vanous A." }, { "name": "Zhang Z." }, { "name": "Sanguinet K." }, { "name": "Garland-Campbell K.A." }, { "name": "Yu J." }, { "name": "Li X." } ], "journal": "Molecular Plant" } } ], "credit": [ { "name": "Xianran Li", "email": "xianran.li@usda.gov", "url": null, "orcidid": "https://orcid.org/0000-0002-4252-6911", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-08-07T17:02:48.364868Z", "lastUpdate": "2023-08-07T17:31:23.486174Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Clustal Omega (EBI)", "description": "Multiple sequence alignment using guide trees and HMM profile-profile techniques.", "homepage": "http://www.ebi.ac.uk/Tools/msa/clustalo/", "biotoolsID": "clustalo_ebi", "biotoolsCURIE": "biotools:clustalo_ebi", "version": [ "1" ], "otherID": [ { "value": "RRID:SCR_001591", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "clustalo", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "clustal", "EBI Tools", "Job Dispatcher Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.ebi.ac.uk/support/", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "http://www.clustal.org/omega/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.ebi.ac.uk/Tools/msa/clustalo/", "type": [ "General" ], "note": null }, { "url": "http://www.clustal.org/omega/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/0471250953.bi0313s48", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Clustal Omega", "abstract": "Clustal Omega is a package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately. It is a complete upgrade and rewrite of earlier Clustal programs. This unit describes how to run Clustal Omega interactively from a command line, although it can also be run online from several sites. The unit describes a basic protocol for taking a set of unaligned sequences and producing a full alignment. There are also protocols for using an external HMM or iteration to help improve an alignment.", "date": "2014-01-01T00:00:00Z", "citationCount": 323, "authors": [ { "name": "Sievers F." }, { "name": "Higgins D.G." } ], "journal": "Current Protocols in Bioinformatics" } }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.", "date": "2022-07-05T00:00:00Z", "citationCount": 376, "authors": [ { "name": "Madeira F." }, { "name": "Pearce M." }, { "name": "Tivey A.R.N." }, { "name": "Basutkar P." }, { "name": "Lee J." }, { "name": "Edbali O." }, { "name": "Madhusoodanan N." }, { "name": "Kolesnikov A." }, { "name": "Lopez R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Des Higgins", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "University College Dublin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "https://www.ebi.ac.uk/Tools/jdispatcher", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "jdispatcher", "additionDate": "2015-01-29T15:47:29Z", "lastUpdate": "2023-08-04T09:36:28.961052Z", "editPermission": { "type": "group", "authors": [ "nandana", "biomadeira" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "epialleleR", "description": "Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package", "homepage": "http://bioconductor.org/packages/epialleleR/", "biotoolsID": "epialleleR", "biotoolsCURIE": "biotools:epialleleR", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3919", "term": "Methylation calling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": null, "cmd": "epialleleR::callMethylation" }, { "operation": [ { "uri": "http://edamontology.org/operation_3207", "term": "Gene methylation analysis" }, { "uri": "http://edamontology.org/operation_3206", "term": "Whole genome methylation analysis" }, { "uri": "http://edamontology.org/operation_0554", "term": "Allele frequency distribution analysis" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [], "note": null, "cmd": "epialleleR::generateCytosineReport\nepialleleR::generateBedReport\nepialleleR::generateVcfReport\nepialleleR::extractPatterns" }, { "operation": [ { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "note": null, "cmd": "epialleleR::simulateBam" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R", "C", "C++" ], "license": "Artistic-2.0", "collectionID": [ "Bioconductor" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/BBCG/epialleleR", "type": [ "Repository" ], "note": null }, { "url": "http://bioconductor.org/packages/epialleleR/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://bioconductor.org/packages/epialleleR/", "type": "Downloads page", "note": null, "version": null }, { "url": "https://doi.org/10.18710/2BQTJP", "type": "Biological data", "note": null, "version": null } ], "documentation": [ { "url": "https://bbcg.github.io/epialleleR/articles/epialleleR.html", "type": [ "Quick start guide" ], "note": null }, { "url": "https://bbcg.github.io/epialleleR/reference/index.html", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1101/2022.06.30.498213", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1001/jamaoncol.2022.3846", "pmid": "36074460", "pmcid": "PMC9459895", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Constitutional BRCA1 Methylation and Risk of Incident Triple-Negative Breast Cancer and High-grade Serous Ovarian Cancer", "abstract": "Importance: About 25% of all triple-negative breast cancers (TNBCs) and 10% to 20% of high-grade serous ovarian cancers (HGSOCs) harbor BRCA1 promoter methylation. While constitutional BRCA1 promoter methylation has been observed in normal tissues of some individuals, the potential role of normal tissue methylation as a risk factor for incident TNBC or HGSOC is unknown. Objective: To assess the potential association between white blood cell BRCA1 promoter methylation and subsequent risk of incident TNBC and HGSOC. Design, Setting, and Participants: This case-control study included women who were participating in the Women's Health Initiative study who had not received a diagnosis of either breast or ovarian cancer before study entrance. A total of 637 women developing incident TNBC and 511 women developing incident HGSOC were matched with cancer-free controls (1841 and 2982, respectively) in a nested case-control design. Cancers were confirmed after central medical record review. Blood samples, which were collected at entry, were analyzed for BRCA1 promoter methylation by massive parallel sequencing. The study was performed in the Mohn Cancer Research Laboratory (Bergen, Norway) between 2019 and 2022. Main Outcomes and Measures: Associations between BRCA1 methylation and incident TNBC and incident HGSOC were analyzed by Cox proportional hazards regression. Results: Of 2478 cases and controls in the TNBC group and 3493 cases and controls in the HGSOC group, respectively, 7 (0.3%) and 3 (0.1%) were American Indian or Alaska Native, 46 (1.9%) and 30 (0.9%) were Asian, 1 (0.04%) and 1 (0.03%) was Native Hawaiian or Pacific Islander, 326 (13.2%) and 125 (3.6%) were Black or African, 56 (2.3%) and 116 (3.3%) were Hispanic, 2046 (82.6%) and 3257 (93.2%) were White, and 35 (1.4%) and 35 (1.0%) were multiracial. Median (range) age at entry was 62 (50-79) years, with a median interval to diagnosis of 9 (TNBC) and 10 (HGSOC) years. Methylated BRCA1 alleles were present in 194 controls (5.5%). Methylation was associated with risk of incident TNBC (12.4% methylated; HR, 2.35; 95% CI, 1.70-3.23; P <.001) and incident HGSOC (9.4% methylated; HR, 1.93; 95% CI, 1.36-2.73; P <.001). Restricting analyses to individuals with more than 5 years between sampling and cancer diagnosis yielded similar results (TNBC: HR, 2.52; 95% CI, 1.75-3.63; P <.001; HGSOC: HR, 1.82; 95% CI, 1.22-2.72; P =.003). Across individuals, methylation was not haplotype-specific, arguing against an underlying cis-acting factor. Within individuals, BRCA1 methylation was observed on the same allele, indicating clonal expansion from a single methylation event. There was no association found between BRCA1 methylation and germline pathogenic variant status. Conclusions and Relevance: The results of this case-control suggest that constitutional normal tissue BRCA1 promoter methylation is significantly associated with risk of incident TNBC and HGSOC, with potential implications for prediction of these cancers. These findings warrant further research to determine if constitutional methylation of tumor suppressor genes are pancancer risk factors..", "date": "2022-11-17T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Lonning P.E." }, { "name": "Nikolaienko O." }, { "name": "Pan K." }, { "name": "Kurian A.W." }, { "name": "Eikesdal H.P." }, { "name": "Pettinger M." }, { "name": "Anderson G.L." }, { "name": "Prentice R.L." }, { "name": "Chlebowski R.T." }, { "name": "Knappskog S." } ], "journal": "JAMA Oncology" } }, { "doi": "10.1101/2023.05.14.23289949", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Oleksii Nikolaienko", "email": null, "url": "https://github.com/BBCG/epialleleR", "orcidid": "https://orcid.org/0000-0002-5910-4934", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null } ], "community": null, "owner": "oleksii.nikolaienko", "additionDate": "2023-08-03T08:30:30.477800Z", "lastUpdate": "2023-08-03T11:21:48.029847Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GeneWise (EBI)", "description": "Compare a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.", "homepage": "http://www.ebi.ac.uk/Tools/psa/genewise/", "biotoolsID": "genewise", "biotoolsCURIE": "biotools:genewise", "version": [ "1" ], "otherID": [ { "value": "RRID:SCR_015054", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "wise", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0491", "term": "Pairwise sequence alignment" }, { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1381", "term": "Sequence alignment (pair)" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "EBI Tools", "Job Dispatcher Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.ebi.ac.uk/support/", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "https://www.ebi.ac.uk/~birney/wise2/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.ebi.ac.uk/Tools/psa/genewise/", "type": [ "General" ], "note": null }, { "url": "https://www.ebi.ac.uk/~birney/wise2/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/gr.10.4.547", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Using GeneWise in the Drosophila annotation experiment", "abstract": "The GeneWise method for combining gene prediction and homology searches was applied to the 2.9-Mb region from Drosophila melanogaster. The results from the Genome Annotation Assessment Project (GASP) showed that GeneWise provided reasonably accurate gene predictions. Further investigation indicates that many of the incorrect gene predictions from GeneWise were due to transposons with valid protein-coding genes and the remaining cases are pseudogenes or possible annotation oversights.", "date": "2000-04-01T00:00:00Z", "citationCount": 277, "authors": [ { "name": "Birney E." }, { "name": "Durbin R." } ], "journal": "Genome Research" } }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.", "date": "2022-07-05T00:00:00Z", "citationCount": 362, "authors": [ { "name": "Madeira F." }, { "name": "Pearce M." }, { "name": "Tivey A.R.N." }, { "name": "Basutkar P." }, { "name": "Lee J." }, { "name": "Edbali O." }, { "name": "Madhusoodanan N." }, { "name": "Kolesnikov A." }, { "name": "Lopez R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Ewan Birney", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "https://www.ebi.ac.uk/Tools/jdispatcher", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "jdispatcher", "additionDate": "2015-01-29T15:47:36Z", "lastUpdate": "2023-07-25T15:25:32.224835Z", "editPermission": { "type": "group", "authors": [ "nandana", "biomadeira" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Wise2DBA (EBI)", "description": "Align two sequences assuming the sequences share colinear conserved blocks separated by gaps.", "homepage": "http://www.ebi.ac.uk/Tools/psa/wise2dba/", "biotoolsID": "wise2dba", "biotoolsCURIE": "biotools:wise2dba", "version": [ "Retired" ], "otherID": [], "relation": [ { "biotoolsID": "wise", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0491", "term": "Pairwise sequence alignment" }, { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1381", "term": "Sequence alignment (pair)" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "EBI Tools" ], "maturity": "Legacy", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.ebi.ac.uk/support/", "type": [ "Helpdesk" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.ebi.ac.uk/Tools/psa/wise2dba/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/gr.9.9.815", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs", "abstract": "A data set of 77 genomic mouse/human gene pairs has been compiled from the EMBL nucleotide database, and their corresponding features determined. This set was used to analyze the degree of conservation of noncoding sequences between mouse and human. A new alignment algorithm was developed to cope with the fact that large parts of noncoding sequences are not alignable in a meaningful way because of genetic drift. This new algorithm, DNA Block Aligner (DBA), finds colinear-conserved blocks that are flanked by nonconserved sequences of varying lengths. The noncoding regions of the data set were aligned with DBA. The proportion of the noncoding regions covered by blocks > 60% identical was 36% for upstream regions, 50% for 5' UTRs, 23% for introns, and 56% for 3' UTRs. These blocks of high identity were more or less evenly distributed across the length of the features, except for upstream regions in which the first 100 bp upstream of the transcription start site was covered in up to 70% of the gene pairs. This data set complements earlier sets on the basis of cDNA sequences and will be useful for further comparative studies.", "date": "1999-09-01T00:00:00Z", "citationCount": 168, "authors": [ { "name": "Jareborg N." }, { "name": "Birney E." }, { "name": "Durbin R." } ], "journal": "Genome Research" } }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. 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Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. 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