isen at molbio.mgh.harvard.edu (Thomas Isenbarger) wrote in message news:<isen-5F54BB.17281208022003 at plato.harvard.edu>...
> Can anyone recommend a UNIX program (for Mac OS X variety) or how to
> tweak the standalone BLAST program to do this. . .
>> I want to search databases with short DNA sequences (15-50 nt) and look
> for exact matches or a few mismatches. I want it to use the whole short
> sequence to do the matching and not just a part of it. I suppose a
> program that looks for PCR primers might work for this, but those
> probably ask for salt concentrations, GC richness, etc.
>> Any help?
>> Thanks
> ---
ALGGEN group has developed a software to search for exact patterns in
dna sequences: MREPATT.
Consecutive Multiple REpeated PATTerns search tool: given a
pattern p, searchs for the exact ocurrences of the patterns
p,pp,ppp,... through a set of DNA sequences. Also several graphycal
representations and mappings are given.
You can work with our database (with several chromosomes) or
submit your files (< 5 Mb fasta file compress in zip format is
strongly recommended). If you are interested in any chromosome that
it isn't in our database, you can send us a request.
With this software you can:
. View the visual map of the ocurrences and zoom
regions.
. View different matching about:
. Chromosomic stathistical distribution .
. Number of ocurrences for each repetition
. Number of theoretical ocurrences for each
repetition
. Differents plots about the search
If you are interested about it and you would test this soft,
you can do it at:
http://www.lsi.upc.es/~alggen
and then in the menu look for:
--> research
--> search
--> mrepatt
An example is available in this site.
After test it on the web, if you wish to obtain the codes for
UNIX,
you can send a request to:
rroset at menta.net.
Thanks
Roman Roset
research assistent and webmaster of :
ALGGEN (Algorithmics and Genetics Group)
www.lsi.upc.es/~alggen
research assistant of CIRI (Cepba - IBM Research Institute):
www.ciri.upc.es
