screening for dinucleotide/trinucleotide repeats in sequence

Gary Williams gwilliam at hgmp.mrc.ac.uk
Wed May 24 04:27:40 EST 2000


In article <7FF0A52BA3D4D211AAC5009027468015087537 at server1.cpc.pitt.edu>,
Gorry, Mike <gorrym at cpc.pitt.edu> wrote:
>
>
>Is anyone aware of a program/algorithm available that will screen large
>segments of 
>sequenced DNA (BACs or PACs) for dinucleotide/trinucleotide repeats that
>have not 
>already been identified?  I have tried checking over the internet but have
>not come up with
>anything.  Pubmed didn't yield anything either.  The only solution at hand
>is to use the FIND
>function to screen each BAC for the desired patterns.  This could take
>forever.  Any information
>will be appreciated.

equicktandem and etandem in EMBOSS


equicktandem - Scans for potential tandem repeats in a nucleotide sequence. 

equicktandem scans a sequence for potential tandem repeats up to a
specified size.  The results can be used to run etandem on the candidate
repeat lengths to identify genuine tandem repeats.  Z

etandem - Looks for tandem repeats in a nucleotide sequence

etandem looks for tandem repeats in a sequence.  It is normally used
after equicktandem has been run to identify potential repeat sizes. 

See:
http://www.sanger.ac.uk/Software/EMBOSS/Apps/equicktandem.shtml
http://www.sanger.ac.uk/Software/EMBOSS/Apps/etandem.shtml
http://www.sanger.ac.uk/Software/EMBOSS/Apps/
http://www.sanger.ac.uk/Software/EMBOSS/

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK






More information about the Bio-www mailing list