[BiO BB] BLAST problems/Questions

Raj Rajkumar.Bondugula at gmail.com
Mon Sep 27 15:24:56 EDT 2004

 I am trying to search a local database with the profile of a sequence
rather than a sequence itself. For this, I first generate profile for
the sequence using 'nr' database and in the second step use the
generated profile to search the local database. I use the 24/7/2004,
windows version BLASTPGP program from NCBI website.

   I was running the following two commands in the same order:

1)'blastpgp -d nr -i seq.txt -j 3 -C profile.bin -o seq.out -a 2'
2)'blastpgp -d sel25culled -i seq.txt -R profile.bin -o seq0.txt -a 2'

  The first run is fine, but the second run produces the following lines:

[NULL_Caption] WARNING: posReadCheckpoint: Attempting to recover data
from previous checkpoint
[NULL_Caption] WARNING: posReadCheckpoint: Data recovered successfully

   Why am I getting these messages, will these messages effect my
results in anyway?

   Also, when I have ungapped alignments while search, I still see
gaps inserted into the protein sequences in the output when I run the
following command:

'blastpgp -d sel25culled -i seq.txt -R profile.bin -o seq0.txt -a 2 -g F'
Why is this happening? is there anyway to have just ungapped alignment
while searching?

Rajkumar Bondugula
Digital Biology Laboratory
316 Engineering Bldg. North
University of Missouri-Columbia

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