On Mon, 30 Nov 1998 16:37:21 -0500,
tendo (tendo at fas.harvard.edu) wrote:
>>Rocky Ho wrote in message <3662D66E.E87FA059 at cuhk.edu.hk>...
>>Hi!
>>>>Is there anyone know a simple program or software which can convert a
>>known sequence into antisense format from 5' to 3'.
>>>#!/usr/bin/perl
># antisense - makes an antisense DNA sequence.
>while (<>) {
> print, next if /^>/;
> tr/acgtuACGTU/tgcaaTGCAA/;
> print;
>}
This would make the anti-sense strand print 3' to 5', wouldn't it? In
a pinch I have used something like the following to print the anti-sense
5' to 3'.
#!/bin/sh
# print antisense
cat $1 | sed y/AGCTUagctu/TCGAAtcgaa/ | rev | tac > $1.rev
A better solution I suppose would be to use Don Gilbert's readseq, which
is available as binaries for a number of platforms, and as source from
ftp://ftp.bio.indiana.edu/molbio/readseq
Ashok
--
Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
aiyar at ebv.oncology.wisc.edu
