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Title: Multiple Whole Genome Alignments and Novel Biomedical Applicationsat the VISTA Portal

Abstract

The VISTA portal for comparative genomics is designed togive biomedical scientists a unified set of tools to lead them from theraw DNA sequences through the alignment and annotation to thevisualization of the results. The VISTA portal also hosts alignments of anumber of genomes computed by our group, allowing users to study regionsof their interest without having to manually download the individualsequences. Here we describe various algorithmic and functionalimprovements implemented in the VISTA portal over the last two years. TheVISTA Portal is accessible at http://genome.lbl.gov/vista.

Authors:
; ; ; ;
Publication Date:
Research Org.:
COLLABORATION - U.Toronto/Canada
OSTI Identifier:
929761
Report Number(s):
LBNL-62511
Journal ID: ISSN 0305-1048; NARHAD; R&D Project: GHPG6C; BnR: 400412000; TRN: US200812%%652
DOE Contract Number:
DE-AC02-05CH11231; NIHU1HL66681B
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nucleic Acids Research; Journal Volume: 35; Related Information: Journal Publication Date: 07/2007
Country of Publication:
United States
Language:
English
Subject:
60; ALIGNMENT; DNA; FUNCTIONALS; VISTA comparative genomics DNA sequence

Citation Formats

Brudno, Michael, Poliakov, Alexander, Minovitsky, Simon, Ratnere,Igor, and Dubchak, Inna. Multiple Whole Genome Alignments and Novel Biomedical Applicationsat the VISTA Portal. United States: N. p., 2007. Web. doi:10.1093/nar/gkm279.
Brudno, Michael, Poliakov, Alexander, Minovitsky, Simon, Ratnere,Igor, & Dubchak, Inna. Multiple Whole Genome Alignments and Novel Biomedical Applicationsat the VISTA Portal. United States. doi:10.1093/nar/gkm279.
Brudno, Michael, Poliakov, Alexander, Minovitsky, Simon, Ratnere,Igor, and Dubchak, Inna. Thu . "Multiple Whole Genome Alignments and Novel Biomedical Applicationsat the VISTA Portal". United States. doi:10.1093/nar/gkm279. https://www.osti.gov/servlets/purl/929761.
@article{osti_929761,
title = {Multiple Whole Genome Alignments and Novel Biomedical Applicationsat the VISTA Portal},
author = {Brudno, Michael and Poliakov, Alexander and Minovitsky, Simon and Ratnere,Igor and Dubchak, Inna},
abstractNote = {The VISTA portal for comparative genomics is designed togive biomedical scientists a unified set of tools to lead them from theraw DNA sequences through the alignment and annotation to thevisualization of the results. The VISTA portal also hosts alignments of anumber of genomes computed by our group, allowing users to study regionsof their interest without having to manually download the individualsequences. Here we describe various algorithmic and functionalimprovements implemented in the VISTA portal over the last two years. TheVISTA Portal is accessible at http://genome.lbl.gov/vista.},
doi = {10.1093/nar/gkm279},
journal = {Nucleic Acids Research},
number = ,
volume = 35,
place = {United States},
year = {Thu Feb 01 00:00:00 EST 2007},
month = {Thu Feb 01 00:00:00 EST 2007}
}
  • Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either on a reference genome, against which all of the other sequences are laid out, or require a one-to-one mapping between the nucleotides of the genomes, preventing the alignment of recently duplicated regions. Both approaches have drawbacks for whole-genome comparisons. In this paper we present a novel symmetric alignment algorithm. The resulting alignments not only represent all of the genomes equally well, but also include all relevant duplications that occurred since the divergence from the lastmore » common ancestor. Our algorithm, implemented as a part of the VISTA Genome Pipeline (VGP), was used to align seven vertebrate and sixDrosophila genomes. The resulting whole-genome alignments demonstrate a higher sensitivity and specificity than the pairwise alignments previously available through the VGP and have higher exon alignment accuracy than comparable public whole-genome alignments. Of the multiple alignment methods tested, ours performed the best at aligning genes from multigene families?perhaps the most challenging test for whole-genome alignments. Our whole-genome multiple alignments are available through the VISTA Browser at http://genome.lbl.gov/vista/index.shtml.« less
  • The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships. Results: We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a frameworkmore » based upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments. Availability: Phylo-VISTA is available at http://www-gsd.lbl. gov/phylovista. It requires an Internet browser with Java Plugin 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu« less
  • The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships. We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a framework basedmore » upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments. Phylo-VISTA is available at http://www-gsd.lbl.gov/phylovista. It requires an Internet browser with Java Plugin 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu/.« less
  • Motivation. The power of multi-sequence comparison forbiological discovery is well established and sequence data from a growinglist of organisms is becoming available. Thus, a need exists forcomputational strategies to visually compare multiple aligned sequencesto support conservation analysis across various species. To be efficientthese visualization algorithms require the ability to universally handlea wide range of evolutionary distances while taking into accountphylogeny Results. We have developed Phylo-VISTA, an interactive tool foranalyzing multiple alignments by visualizing the similarity of DNAsequences among multiple species while considering their phylogenicrelationships. Features include a broad spectrum of resolution parametersfor examining the alignment and the ability to easilymore » compare any subtreeof sequences within a complete alignment dataset. Phylo-VISTA uses VISTAconcepts that have been successfully applied previously to a wide rangeof comparative genomics data analysis problems. Availability Phylo-VISTAis an interactive java applet available for downloading athttp://graphics.cs.ucdavis.edu/~;nyshah/Phylo-VISTA. It is also availableon-line at http://www-gsd.lbl.gov/phylovista and is integrated with theglobal alignment program LAGAN athttp://lagan.stanford.edu.Contactphylovista@lbl.gov« less