Question: Old Blastall Vs New Blastall
0
gravatar for User 4143
9.4 years ago by
User 414320
User 414320 wrote:

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)


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.

database blast • 2.8k views
ADD COMMENTlink modified 9.2 years ago by Neilfws48k • written 9.4 years ago by User 414320
1
gravatar for Chris Evelo
9.4 years ago by
Chris Evelo10k
Maastricht, The Netherlands
Chris Evelo10k wrote:

You might want to check this question:

Help With Formatdb And Blast All

ADD COMMENTlink modified 12 months ago by zx87549.6k • written 9.4 years ago by Chris Evelo10k
1
gravatar for Neilfws
9.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink modified 12 months ago by RamRS30k • written 9.4 years ago by Neilfws48k
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