MUltiple sequence Alignment Software

Peter Rice pmr at sanger.ac.uk
Mon Oct 2 04:26:32 EST 1995


In article <44hklg$81p at mark.ucdavis.edu> ez041797 at dale.ucdavis.edu (Jean-Manuel Henry) writes:
>   I have used gcg's "pileup" and "best-fit" to do some sequence alignment. 
>   I am looking for a program (any platform) which is a mix between these two
>   utilities.  "Best-fit" wil draw pairing lines between any two sequences 
>   so that it is relatively easy to identify stretches of homogeneity and 
>   heterogeneity, unfortunately it will only pair two sequences at a time. 
>   "Pile-up" will pair multiple sequences at oncer , but will not indicate 
>   pairing lines (i.e. you must go through the aligned sequences by hand to 
>   find pair or mismatches) . I would like a program that can draw pairing 
>   lines between multiple sequences.  Any ideas would be greatly 
>   appreciated. 

Th eproblem with "pairing lines" is that it is only easy to draw them
between two sequences.

For multiple sequences, the matching residues are usually indicated by
drawing boxes around all the matching residues.

Two programs, PRETTYPLOT and PRETTYBOX, in the EGCG "extended GCG" package
do this, and read pileup's MSF files as input.

EGCG is available from ftp://ftp.sanger.ac.uk/pub/pmr/egcg8/

More information about EGCG is on my home page http://www.sanger.ac.uk/~pmr/

--
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Peter Rice                           | Informatics Division
E-mail: pmr at sanger.ac.uk             | The Sanger Centre
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