Old Blastall Vs New Blastall

Question

[User 4143]

I've been using blast 2.2.15 for a while, and I recently downloaded blast 2.2.25 on my new computer. I wanted to test the new version of blastall with a lamprey genome database and sequence that works on my old computer; however, the new blastall doesn't seem to be doing anything.

For the command,

blastall -p tblastn -d supercontigs.fa.pal -i fgah.fa

The output is:

TBLASTN 2.2.25 [Feb-01-2011]

Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.

Query= FIBRINOGEN GAMMA CHAIN, HUMAN (411 letters)

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Since the output stops before mentioning the database, is my old database format incompatible with the new blastall? I attempted to formatdb my database, but blastall still didn't work. Perhaps I'm improperly using formatdb? I haven't been able to find a lamprey database to redownload and formatdb from scratch.

Answer 1

[Chris Evelo]

You might want to check this question:

Help With Formatdb And Blast All

Answer 2

[Neilfws]

Are you using BLAST 2.2.25 (from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.25/) or BLAST 2.2.25+ (from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.25/) ?

If the former, database format should not be an issue, provided that formatdb ran without error. Did you check the output in formatdb.log?

Your blastall command looks odd: usually the .pal suffix would not be part of the database name. If the database files contain .fa.*, try "-d supercontigs.fa".

If the latter you need to create databases using the new command makeblastdb.