[BiO BB] database search/alignment with ciruclar molecules?

Ethan Strauss ethan.strauss at promega.com
Tue Feb 19 11:29:25 EST 2008

	I have created a database which holds plasmid sequences and I am
running into an issue with doing database similarity searches due to the
fact that the molecules are circular. Right now, I am using a brute
force approach where I pull each plasmid out of the database and perform
a Smith Watermann alignment to it to find similar sequences. I plan to
go to BLAST sometime soon. Anyway, I am having problems due to the fact
that the molecules involved are circular, but the alignment treats them
as linear. For Smith Watermann, I know I can deal with circularity by
treating the sequences as dimers, but I don't know if that is the best
way to approach it and it will make something which is incredibly slow
incredibly slower! I would appreciate any thoughts on this issue. 

Ethan Strauss Ph.D.
Bioinformatics Scientist
Promega Corporation
2800 Woods Hollow Rd.
Madison, WI 53711
ethan.strauss at promega.com

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