[BiO BB] BLAST and multiple section alignment

Theodore H. Smith delete at elfdata.com
Sat Feb 25 12:25:27 EST 2006

I'm not sure if I got this correct, so let me know if this isn't  
true. I'm just asking for confirmation here.

My question: It seems that BLAST does not generate multiple section  
alignments? Is this true or not?

By multiple section alignments, I  mean for example when the head of  
a gene is moved to the middle of a gene. A very sophisticated gene  
searcher could generate a stronger hit for such a case, than simply  
returning the best alignment, because there will now be multiple  
alignments within the two genes that we are comparing.


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