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
