Blast and fmerge Problems

Alan Williams Alan at MolBio.org
Wed Aug 18 12:21:12 EST 1999

Hello All,

I am having problems with blast recognizing sequences added with
fmerge.  What I am doing:

# Setup the initial fasta file for blast searchers
% formatdb -t zmdbest -i zmdbest.Uptodate.est.fasta \
        -l zmdbest.formatdb.log -p F  -o T -n zmdbest

# Run fmerge on the original fasta file
% fmerge -t 1 -n zmdbest.Uptodate.est.fasta -i zmdbest.index

At this point all is well.  Blast recognizes all the sequences in
zmdbest. Now if I download some new sequences to add I do the 

# Run fmerge to add new sequences to the original fasta file
% fmerge -l 10-1-1999.fmerge.log -t 3 -m 10-1-1999.fasta \
	-n zmdbest.Uptodate.est.fasta -i zmdbest.index

fmerge reports that the sequences have been added, and a simple 
cat zmdbest.Uptodate.est.fasta | grep -c '' confirms that the
sequences are in there.  Now if I run blast, it still reports
the original number of sequences rather than the original plus the
update.  If I rerun the formatdb command at this point, blast will
then recognize the new sequences that were added.

Any ideas on what is going wrong here?

Alan Williams

ps -- This is on a Linux Redhat 6.0 system on a Pentium II with 
      a custom build of the NCBI libraries and blast binaries.

Alan Williams                      Where observation is concerned,
Alan at MolBio.org                    chance favors the prepared mind.
http://www.MolBio.org/cv/                         -- Louis Pasteur
   **  University of California, Botany Department, Riverside  **

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net