[BiO BB] Search reverse repeat

Zhang, Yuanji yjzhang at noble.org
Tue Jun 1 11:46:54 EDT 2004

Which similarity search program will align reverse repeats in the genome?
For example, if I have 2 sequences, 
>Seq A


>Seq B

Seq A and Seq B are reverse repeats to each other. 

BLAST does not align A and B. 

I can manipulate the sequences by reversing one seq and then align, but I'd
like to know whether there is a program that align A and B without extra
sequence manipulation. Any information is appreciated.

More information about the BBB mailing list