[BiO BB] BLAST problems/Questions

[Aaron J. Mackey]

>    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 ...

-Aaron