DNA sequence alignments

N. Linford nantzee at u.washington.edu
Wed Dec 3 14:20:30 EST 1997


Thank you for your replies. Two people suggested programs that box similar
residues. However, what I am looking for is a program that will box
DOMAINS (putative transmembrane domains, etc). When you retrieve a
sequence from swissprot it lists these domains by amino acid number so it
would theoretically be possible to box these domains in alignments of
similar proteins.

On 3 Dec 1997, Wolfgang Schechinger wrote:

=>Boxshade does what you want!
=>
=>http://www.blocks.fhcrc.org/~kinesin/KLC2BoxShade.html
=>
=>> does anyone know of a program which would draw boxes around the DNA
=>> segments coding for protein domains in sequence alignments? It is
=>> quite a pain to transfer the seqences and edit them by hand. thanks!
=>> Nancy
=>




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