[BiO BB] BLAST problems/Questions
Aaron J. Mackey
amackey at pcbi.upenn.edu
Mon Sep 27 15:32:10 EDT 2004
> Why am I getting these messages, will these messages effect my
> results in anyway?
These are "positive" notifications: everything worked fine. Checkpoint
file usage is still considered "experimental" by NCBI, so these
"debugging" statements are still there. Ignore them (unless it says
"unsuccessful", of course).
> Why is this happening? is there anyway to have just ungapped alignment
> while searching?
BLAST is a gap-capable algorithm; the fact that you've given it a
profile instead of a "flat" scoring matrix doesn't change anything. If
you'd like to prevent gaps, try raising the gap penalties ...
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