short sequence matching

Roman Roset r.roset at menta.net
Wed Feb 19 04:46:09 EST 2003

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
                . View different matching about:
                        . Chromosomic stathistical distribution .
                        . Number of ocurrences for each repetition
                        . Number of theoretical ocurrences for each
                        . Differents plots about the search

        If you are interested about it and you would test this soft,
you can do it at:
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
you can send a request to:
         rroset at menta.net.

Roman Roset
research assistent and webmaster of :
               ALGGEN (Algorithmics and Genetics Group)
research assistant of CIRI (Cepba - IBM Research Institute):

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