Phylo-VISTA: An interactive visualization tool for multiple DNAsequence alignments

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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 easily ... continued below

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Shah, Nameeta; Couronne, Olivier; Pennacchio, Len A.; Brudno,Michael; Batzoglou, Serafim; Bethel, E. Wes et al. April 25, 2003.

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Description

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 easily 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

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  • Journal Name: Bioinformatics; Journal Volume: 20; Journal Issue: 5; Related Information: Journal Publication Date: 03/22/2004

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  • Report No.: LBNL--52539
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 918099
  • Archival Resource Key: ark:/67531/metadc884210

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  • April 25, 2003

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  • Sept. 22, 2016, 2:13 a.m.

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Shah, Nameeta; Couronne, Olivier; Pennacchio, Len A.; Brudno,Michael; Batzoglou, Serafim; Bethel, E. Wes et al. Phylo-VISTA: An interactive visualization tool for multiple DNAsequence alignments, article, April 25, 2003; United States. (digital.library.unt.edu/ark:/67531/metadc884210/: accessed August 20, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.