{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T15:27:27Z","timestamp":1771342047871,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: With the ubiquitous generation of complete genome assemblies for a variety of species, efficient tools for whole-genome alignment along with user-friendly visualization are critically important. Our VISTA family of tools for comparative genomics, based on algorithms for pairwise and multiple alignments of genomic sequences and whole-genome assemblies, has become one of the standard techniques for comparative analysis. Most of the VISTA programs have been implemented as Web-accessible servers and are extensively used by the biomedical community. In this manuscript, we introduce GenomeVISTA: a novel implementation that incorporates most features of the VISTA family\u2014fast and accurate alignment, visualization capabilities, GUI and analytical tools within a stand-alone software package. GenomeVISTA thus provides flexibility and security for users who need to conduct whole-genome comparisons on their own computers.<\/jats:p>\n               <jats:p>Availability and implementation: Implemented in Perl, C\/C++ and Java, the source code is freely available for download at the VISTA Web site: http:\/\/genome.lbl.gov\/vista\/<\/jats:p>\n               <jats:p>Contact: \u00a0avpoliakov@lbl.gov or ildubchak@lbl.gov<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu355","type":"journal-article","created":{"date-parts":[[2014,5,24]],"date-time":"2014-05-24T04:01:20Z","timestamp":1400904080000},"page":"2654-2655","source":"Crossref","is-referenced-by-count":32,"title":["GenomeVISTA\u2014an integrated software package for whole-genome alignment and visualization"],"prefix":"10.1093","volume":"30","author":[{"given":"Alexandre","family":"Poliakov","sequence":"first","affiliation":[{"name":"1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, 2 Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, 3 Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and 4 Genomics Division, LBNL, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Justin","family":"Foong","sequence":"additional","affiliation":[{"name":"1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, 2 Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, 3 Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and 4 Genomics Division, LBNL, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Brudno","sequence":"additional","affiliation":[{"name":"1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, 2 Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, 3 Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and 4 Genomics Division, LBNL, Berkeley, CA 94720, USA"},{"name":"1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, 2 Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, 3 Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and 4 Genomics Division, LBNL, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inna","family":"Dubchak","sequence":"additional","affiliation":[{"name":"1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, 2 Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, 3 Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and 4 Genomics Division, LBNL, Berkeley, CA 94720, USA"},{"name":"1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, 2 Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, 3 Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and 4 Genomics Division, LBNL, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,5,23]]},"reference":[{"key":"2023012711553746900_btu355-B1","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1101\/gr.789803","article-title":"AVID: a global alignment program","volume":"13","author":"Bray","year":"2003","journal-title":"Genome Res."},{"key":"2023012711553746900_btu355-B2","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1101\/gr.926603","article-title":"LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA","volume":"13","author":"Brudno","year":"2003","journal-title":"Genome Res."},{"key":"2023012711553746900_btu355-B3","doi-asserted-by":"crossref","first-page":"i54","DOI":"10.1093\/bioinformatics\/btg1005","article-title":"Glocal alignment: finding rearrangements during alignment","volume":"19","author":"Brudno","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012711553746900_btu355-B4","doi-asserted-by":"crossref","first-page":"D646","DOI":"10.1093\/nar\/gkr990","article-title":"The UCSC archaeal genome browser: 2012 update","volume":"40","author":"Chan","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012711553746900_btu355-B5","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1038\/nbt.1637","article-title":"Comparative assessment of methods for aligning multiple genome sequences","volume":"28","author":"Chen","year":"2010","journal-title":"Nat. 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