Convert to Antisense sequence

Ashok Aiyar aiyar at ebv.oncology.wisc.edu
Mon Nov 30 18:24:18 EST 1998

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>...
>>Is there anyone know a simple program or software which can convert a
>>known sequence into antisense format from 5' to 3'.
># 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'.

# 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

Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
aiyar at ebv.oncology.wisc.edu

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net