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Questions about fasta searches?

Ramzi Azzam uramzzzz at mcl.ucsb.edu
Fri Nov 18 19:33:06 EST 1994


I would like to know if there is a way to restrict the search when 
using fasta. my problem is that I want to search using a 26bp 
segment of DNA that contains a central CG bp. I want each sequence
selected by fasta to contain this CG and to penalize any sequence not 
containing the CG such that it does not appear in the best score list.
If any one has any ideas on how to do this, it will be greatly 
appreciated and thanks in advance.
my e-mail address is uramzzzz at mcl.mcl.ucsb.edu




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