IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

Gene searching contain microsatellite in coding region

Wilson CHAN netson at hotmail.com
Mon Dec 4 09:59:54 EST 2000

Dear all,

We would like to find as much as possible of the human genes that contain 
mononucleotide repeat (above 5, just like microsatellite in coding region) 
and we don't have any specific probe sequence for searching.
Therefore the only sequence that we can use is the mononucleotide repeat we 
started the search from nucleotide BLAST human ESTs database.  The problem 
that we encountered is if we set the BLAST search filter to low complexity, 
we get nothing from the search.  If we disable the low complexity, we get 
some result but some of them are derivated from same clone and some of them 
are unlikely in coding sequence.  We have to screen thousands of the search 
by naked eyes.

My question is what is the effective ways to find the genes that mentioned 
above?  (How to set the blast search to optimize the result or is there any 
software or database that help to perform such searching?)

Thank you very much

Best Regards,

Wilson CHAN
Get more from the Web.  FREE MSN Explorer download : http://explorer.msn.com


More information about the Bio-www mailing list

Send comments to us at archive@iubioarchive.bio.net