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VISTA: computational tools for comparative genomics

Frazer, Kelly A. and Pachter, Lior and Poliakov, Alexander and Rubin, Edward M. and Dubchak, Inna (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Research, 32 (Suppl. 2). W273-W279. ISSN 0305-1048. PMCID PMC441596. https://resolver.caltech.edu/CaltechAUTHORS:20170308-140652072

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Abstract

Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/vista/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, to submit their own sequences of interest to several VISTA servers for various types of comparative analysis and to obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/nar/gkh458DOIArticle
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkh458PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC441596/PubMed CentralArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2004, the authors. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. Received February 16, 2004; Revised and Accepted April 26, 2004. We are grateful to Simon Minovitsky, Shyam Prabhakar, Michael Teplitsky and Dmitriy Ryaboy for ongoing development, maintenance and support of all our tools. The VISTA project is a collaborative effort of a large group of scientists and engineers. Among contributors are Nicolas Bray (the author of AVID and contributor to the design of whole-genome alignment strategies), Michael Brudno (contributor to MLAGAN and multiple whole-genome alignment), Nameeta Shah (the author of Phylo-VISTA), Olivier Couronne (contributor to whole-genome alignment), Gabriela Loots (rVISTA), Ivan Ovcharenko (contributor to rVISTA and whole-genome alignment), Chris Mayor (contributor to mVISTA) and Brian Klock and Lila Tretikov (VISTA Browser). Our special thanks to the biologists of the Genomics Division at LBNL (Dario Boffelli, Jim Bristow, Jan-Fang Cheng, Marcelo Nobrega, Len Pennacchio, James Priest and many others) for their help, support and critical comments. This project was partially supported by the Programs for Genomic Applications grant from the NHLBI/NIH and the Office of Biological and Environmental Research, Office of Science, US Department of Energy.
Funders:
Funding AgencyGrant Number
National Heart, Lung, and Blood InstituteUNSPECIFIED
Department of Energy (DOE)UNSPECIFIED
Issue or Number:Suppl. 2
PubMed Central ID:PMC441596
Record Number:CaltechAUTHORS:20170308-140652072
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170308-140652072
Official Citation:Kelly A. Frazer, Lior Pachter, Alexander Poliakov, Edward M. Rubin, Inna Dubchak; VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004; 32 (suppl_2): W273-W279. doi: 10.1093/nar/gkh458
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74918
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:08 Mar 2017 22:22
Last Modified:24 Feb 2020 10:30

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