LALNVIEW :
A graphical viewer for pairwise alignments

LALNVIEW is a graphical program for visualizing local alignments between two sequences (protein or nucleic acids) [reference]. Sequences are represented by colored rectangles to give an overall picture of the similarities between the two sequences. Blocks of similarity between the two sequences are colored according to the degree of identity between the two segments.

Click here to see what it looks like.

LALNVIEW is also able to display sequence features (active site, domain, motif, propeptide, exon, intron, promoter, etc.) along with the alignment. This allows one to make the link between sequence similarity and known functions.

LALNVIEW can be used through the ExPASy WWW server to compare protein sequences, or through the ACNUC server for nucleic acid sequences. Sequences can be entered by the user or extracted from SWISS-PROT, GenBank, EMBL or HOVERGEN.

When using LALNVIEW through these servers, sequence features are automatically extracted from database annotations and displayed with the alignment.

By clicking on a block, the user can visualize the corresponding local alignment.

A domain can be repeated in a sequence: iterative clicking on one block will successively display all the similar blocks that occur in the other sequence.

LALNVIEW is available for UNIX, Mac and PC on the ExPASy anonymous FTP server.

For more details, read the documentation.

Laurent Duret
Laboratoire BGBP - CNRS UMR 5558
Université Claude Bernard - Lyon 1
43 Bd du 11 Novembre 1918
F-69622 Villeurbanne Cedex
France

Electronic mail address: duret@biomserv.univ-lyon1.fr
WWW server: http://www.expasy.ch/