Need Sequence Similarity Search tool

Kevin Matthew Jude jude at ANCHOR.CHEM.UPENN.EDU
Mon Aug 16 14:44:36 EST 1999


I am looking for a sequence similarity search tool, preferably
web-based, but anything will do, that will search nucleotide sequence
databases and return relatively long matches ( +- 100 nt ) that may have
relatively low sequence identity ( +- 50%).  

My problem is, when I enter my sequence of interest (102 nt) in BLASTn,
it returns only short, high identity sequences (ie, 15 bp, 95%
identity).  Even by significantly increasing my expect value and
allowing a large number of hits, BLAST won't return long sequences
unless they have very high sequence identity.

TIA for any advice -
Kevin




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