{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T19:14:10Z","timestamp":1770837250667,"version":"3.50.1"},"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T00:00:00Z","timestamp":1770768000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["UM1TR005121"],"award-info":[{"award-number":["UM1TR005121"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1013919","type":"journal-article","created":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T18:26:21Z","timestamp":1770834381000},"page":"e1013919","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Ten quick tips for using the NIH Comparative Genomics Resource"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1169-3079","authenticated-orcid":true,"given":"Eric S.","family":"Tvedte","sequence":"first","affiliation":[]},{"given":"Cecilia","family":"Arighi","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4105-9220","authenticated-orcid":true,"given":"Matthew B.","family":"Carson","sequence":"additional","affiliation":[]},{"given":"Luke V.","family":"Rasmussen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8420-5254","authenticated-orcid":true,"given":"Kristi","family":"Holmes","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9311-9745","authenticated-orcid":true,"given":"Terence D.","family":"Murphy","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2026,2,11]]},"reference":[{"issue":"1","key":"pcbi.1013919.ref001","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1186\/s12864-023-09643-4","article-title":"The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health","volume":"24","author":"K Bornstein","year":"2023","journal-title":"BMC Genomics"},{"issue":"1","key":"pcbi.1013919.ref002","article-title":"Ten simple rules for using public biological data for your research","volume":"19","author":"VH Oza","year":"2023","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"pcbi.1013919.ref003","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/s13059-024-03198-7","article-title":"Rapid and sensitive detection of genome contamination at scale with FCS-GX","volume":"25","author":"A Astashyn","year":"2024","journal-title":"Genome Biol"},{"key":"pcbi.1013919.ref004","doi-asserted-by":"crossref","first-page":"33","DOI":"10.12688\/wellcomeopenres.20730.1","article-title":"MarkerScan: separation and assembly of cobionts sequenced alongside target species in biodiversity genomics projects","volume":"9","author":"E Vancaester","year":"2024","journal-title":"Wellcome Open Res"},{"issue":"1","key":"pcbi.1013919.ref005","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa153","article-title":"Significantly improving the quality of genome assemblies through curation","volume":"10","author":"K Howe","year":"2021","journal-title":"Gigascience"},{"issue":"7856","key":"pcbi.1013919.ref006","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/s41586-021-03451-0","article-title":"Towards complete and error-free genome assemblies of all vertebrate species","volume":"592","author":"A Rhie","year":"2021","journal-title":"Nature"},{"issue":"3","key":"pcbi.1013919.ref007","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/j.tig.2022.10.005","article-title":"A proposed metric set for evaluation of genome assembly quality","volume":"39","author":"P Wang","year":"2023","journal-title":"Trends Genet"},{"issue":"5","key":"pcbi.1013919.ref008","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1101\/gr.278090.123","article-title":"BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA","volume":"34","author":"L Gabriel","year":"2024","journal-title":"Genome Res"},{"key":"pcbi.1013919.ref009","article-title":"The international nucleotide sequence database collaboration (INSDC): enhancing global participation","volume":"53","author":"I Karsch-Mizrachi","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1013919.ref010","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae1114","article-title":"GenBank 2025 update","volume":"53","author":"EW Sayers","year":"2025","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pcbi.1013919.ref011","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1038\/s41597-024-03571-y","article-title":"Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets","volume":"11","author":"NA O\u2019Leary","year":"2024","journal-title":"Sci Data"},{"issue":"1","key":"pcbi.1013919.ref012","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/veaf051","article-title":"Insights into diversity, host range, and evolution of iflaviruses in Lepidoptera through transcriptome mining","volume":"11","author":"D van Valkengoed","year":"2025","journal-title":"Virus Evol"},{"key":"pcbi.1013919.ref013","doi-asserted-by":"crossref","first-page":"1475003","DOI":"10.3389\/fimmu.2024.1475003","article-title":"Deciphering Gorilla gorilla gorilla immunoglobulin loci in multiple genome assemblies and enrichment of IMGT resources","volume":"15","author":"C Debbagh","year":"2024","journal-title":"Front Immunol"},{"issue":"1","key":"pcbi.1013919.ref014","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1186\/s12864-025-11252-2","article-title":"Krait2: a versatile software for microsatellite investigation, visualization and marker development","volume":"26","author":"L Du","year":"2025","journal-title":"BMC Genomics"},{"key":"pcbi.1013919.ref015","article-title":"Overcoming the widespread flaws in the annotation of vertebrate selenoprotein genes in public databases","author":"M Tic\u00f3","year":"2024","journal-title":"bioRxiv"},{"issue":"19","key":"pcbi.1013919.ref016","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"FA Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"issue":"3","key":"pcbi.1013919.ref017","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"issue":"17","key":"pcbi.1013919.ref018","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"SF Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"pcbi.1013919.ref019","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1093\/bioinformatics\/bty833","article-title":"Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows","volume":"35","author":"N Shah","year":"2019","journal-title":"Bioinformatics"},{"issue":"15","key":"pcbi.1013919.ref020","doi-asserted-by":"crossref","first-page":"2697","DOI":"10.1093\/bioinformatics\/bty1018","article-title":"Commonly misunderstood parameters of NCBI BLAST and important considerations for users","volume":"35","author":"RA Gonz\u00e1lez-Pech","year":"2019","journal-title":"Bioinformatics"},{"issue":"15","key":"pcbi.1013919.ref021","doi-asserted-by":"crossref","first-page":"2699","DOI":"10.1093\/bioinformatics\/bty1026","article-title":"Reply to the paper: misunderstood parameters of NCBI BLAST impacts the correctness of bioinformatics workflows","volume":"35","author":"TL Madden","year":"2019","journal-title":"Bioinformatics"},{"key":"pcbi.1013919.ref022","unstructured":"National Center for Biotechnology Information. BLAST Homepage and Selected Search Pages; 2019. Available from: https:\/\/ftp.ncbi.nlm.nih.gov\/pub\/factsheets\/HowTo_BLASTGuide.pdf"},{"key":"pcbi.1013919.ref023","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae979","article-title":"Database resources of the National Center for Biotechnology Information in 2025","volume":"53","author":"EW Sayers","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1013919.ref024","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkac1032","article-title":"Database resources of the National Center for Biotechnology Information in 2023","volume":"51","author":"EW Sayers","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pcbi.1013919.ref025","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1186\/s12859-023-05245-9","article-title":"ElasticBLAST: accelerating sequence search via cloud computing","volume":"24","author":"C Camacho","year":"2023","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"pcbi.1013919.ref026","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1101\/gr.266932.120","article-title":"Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)","volume":"31","author":"SH Rangwala","year":"2021","journal-title":"Genome Res"},{"issue":"5","key":"pcbi.1013919.ref027","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3002405","article-title":"The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments","volume":"22","author":"SH Rangwala","year":"2024","journal-title":"PLoS Biol"},{"issue":"1","key":"pcbi.1013919.ref028","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/S0168-9525(99)01882-X","article-title":"Introducing RefSeq and LocusLink: curated human genome resources at the NCBI","volume":"16","author":"KD Pruitt","year":"2000","journal-title":"Trends Genet"},{"key":"pcbi.1013919.ref029","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"NA O\u2019Leary","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1013919.ref030","article-title":"NCBI RefSeq: reference sequence standards through 25 years of curation and annotation","volume":"53","author":"T Goldfarb","year":"2024","journal-title":"Nucleic Acids Research"},{"key":"pcbi.1013919.ref031","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gku1055","article-title":"Gene: a gene-centered information resource at NCBI","volume":"43","author":"GR Brown","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pcbi.1013919.ref032","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003542","article-title":"Ten simple rules for the care and feeding of scientific data","volume":"10","author":"A Goodman","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1013919.ref033","unstructured":"National Center for Biotechnology Information. How do I cite NCBI services and databases?. Available from: https:\/\/support.nlm.nih.gov\/kbArticle\/?pn=KA-03391"},{"key":"pcbi.1013919.ref034","volume-title":"Citing medicine: The NLM style guide for authors, editors, and publishers","author":"K Patrias","year":"2018","edition":"2"},{"issue":"3","key":"pcbi.1013919.ref035","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0000308","article-title":"Sharing detailed research data is associated with increased citation rate","volume":"2","author":"HA Piwowar","year":"2007","journal-title":"PLoS One"},{"issue":"10","key":"pcbi.1013919.ref036","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1038\/s41576-020-0257-5","article-title":"Responsible, practical genomic data sharing that accelerates research","volume":"21","author":"JB Byrd","year":"2020","journal-title":"Nat Rev Genet"},{"key":"pcbi.1013919.ref037","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"MD Wilkinson","year":"2016","journal-title":"Sci Data"},{"issue":"9","key":"pcbi.1013919.ref038","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1011369","article-title":"Ten quick tips for building FAIR workflows","volume":"19","author":"C de Visser","year":"2023","journal-title":"PLoS Comput Biol"},{"issue":"8","key":"pcbi.1013919.ref039","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae477","article-title":"AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality","volume":"40","author":"U Rashid","year":"2024","journal-title":"Bioinformatics"},{"key":"pcbi.1013919.ref040","article-title":"Pipeasm: a tool for automated large chromosome-scale genome assembly and evaluation","author":"BM Silva","year":"2024","journal-title":"bioRxiv"},{"issue":"5","key":"pcbi.1013919.ref041","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btaf175","article-title":"Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly","volume":"41","author":"L Obinu","year":"2025","journal-title":"Bioinformatics"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013919","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T18:26:25Z","timestamp":1770834385000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013919"}},"subtitle":[],"editor":[{"given":"Patricia M","family":"Palagi","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2026,2,11]]},"references-count":41,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2,11]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1013919","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,11]]}}}