Bioinformatics.org
[NEU MS in Bioinformatics]
Not logged in
  • Log in
  • Bioinformatics.org
    Membership (37461+) Group hosting [?]
  • Wiki
  • Franklin Award
  • Sponsorships
  • Careers
    About bioinformatics
    Bioinformatics training
    Bioinformatics jobs

    Research
    All information groups
    Online databases Online analysis tools Online education tools More tools

    Development
    All software groups
    FTP repository
    SVN & CVS repositories [?]
    Mailing lists

    Forums
    News & Commentary
  • Submit
  • Archives
  • Subscribe

  • Jobs Forum
    (Career Center)
  • Submit
  • Archives
  • Subscribe
  • News & Commentary - Message forums

    Software: JProfileGrid for visualizing large multiple sequence alignments
    Submitted by Alberto Roca; posted on Friday, January 16, 2009 (1 comment)

    Comparative nanoanatomy and phylogenetic studies of macromolecules depend upon multiple sequence alignments (MSAs). However, large data sets are no longer manageable for visualization and investigation using the traditional stacked sequence alignment representation.

    We introduce ProfileGrids that represent a MSA as a matrix color-coded according to the residue frequency occurring at each column position. JProfileGrid is a Java application for computing and analyzing ProfileGrids. A dynamic interaction with the alignment information is achieved by changing the ProfileGrid color scheme, by extracting sequence subsets at selected residues of interest, and by relating alignment information to residue physical properties. Conserved family motifs can be identified by the overlay of similarity plot calculations on a ProfileGrid. Figures suitable for publication can be generated from the saved spreadsheet output of the colored matrices as well as by the export of conservation information for use in the PyMOL molecular visualization program.

    AVAILABILITY

    Download at www.profilegrid.org

    ARTICLE:
    "ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family"
    Alberto I Roca*, Albert E Almada, Aaron C Abajian
    BMC Bioinformatics 9:554 (2008)
    www.biomedcentral.com/1471[...]tract

    REQUESTING COMMENTS

    Any feedback on the ProfileGrid paradigm and the Java software are appreciated. We are especially interested in any citations to novel alignment representation paradigms that were _not_ mentioned in the background section of our paper. Specifically, are there any other alignment visualization paradigms besides the following: the traditional stacked sequence lists; boxing, coloring, & shading of stacked sequences; regular expressions; major components; sequence logos; graphical "overviews" (such as by Jalview or CINEMA); similarity value plots, and ProfileGrids.

    Expanded view | Monitor forum | Save place

    Message
    Updated JProfileGrid software
    Submitted by Alberto Roca; posted on Sunday, June 21, 2009
    New JProfileGrid version (v1.2.1) fixes bug that prevented command-line version from working.



    Post a followup to this message:
    You have to be logged in to post a reply.
    Thread view
    Updated JProfileGrid software
    Submitted by Alberto Roca; posted on Sunday, June 21, 2009
    New JProfileGrid version (v1.2.1) fixes bug that prevented command-line version from working.

     

    Copyright © 2016 · Scilico, LLC