Pairwise alignment computing and visualization

Guy Perriere perriere at biomserv.univ-lyon1.fr
Wed Apr 10 02:25:20 EST 1996


    It  is  now possible to perform pairwise local alignments on
    proteins  and  on  nucleic  acids  on the two World Wide Web
    servers  ExPASy  and WWW-Query. Alignments are computed with
    the SIM (proteins) and LFASTA (nucleic acids) algorithms.

    To  ease   the interpretation of the results returned by SIM
    and LFASTA, the users may use the LALNVIEW program. LALNVIEW
    allows  to  represent  sequences  by colored rectangles that
    give  an overall picture of the similarities between the two
    sequences.  Blocks  containing similar fragments are colored
    according  to  the  degree  of  similarity  between  the two
    segments.  Also,  when   aligning sequences from SWISS-PROT,
    EMBL,  GenBank  or  Hovergen  data  banks, it is possible to
    include   in the alignment a graphical view of the sequences
    features. 

    LALNVIEW  can  be  used  as a standalone application or as a
    helper  application  when using ExPASy or WWW-Query. In this
    case,  prospective users must configure their World Wide Web
    browser  in a way to make it able to recognize the MIME-type
    associated  to  the  data  returned  by  LALNVIEW: chemical/
    x-aln2. For instance, UNIX users have to modify the .mailcap
    file located in their home directory by adding the following
    line:

    chemical/x-aln2; lalnview %s

    Binaries of LALNVIEW for Macintosh, PC and compatibles, SUN,
    DEC  Alpha,  IBM RS/6000, SGI and HP computers are available
    at URL:

    ftp://expasy.hcuge.ch/pub/lalnview

    The  page  on  the  ExPASy  server allowing to align protein
    sequences can be reached at URL:

    http://expasy.hcuge.ch/sprot/sim-prot.html

    The  page  on the WWW-Query server allowing to align nucleic
    acids sequences can be reached at URL:

    http://acnuc.univ-lyon1.fr/lfasta.html


--
Guy Perriere
Laboratoire BGBP - UMR CNRS 5558
Universite Claude Bernard - Lyon 1
F-69622 Villeurbanne Cedex






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