Question: A trouble in using psiblast, blastdbcmd outputs empty file. why?
gravatar for ygxing1
19 months ago by
ygxing10 wrote:

Hi, every one!

I use psiblast to search the homologous protein sequences. Then use blastdbcmd to extract the exact homologous sequences based on the output file of psiblast. BUT I met a weird trouble as follows.

================ Below will get one seq output ===========

blastdbcmd -entry 99 -db ./db/test -dbtype prot -outfmt %f -out test.hits.fa

================= Below will get empty output ================

blastdbcmd -entry_batch fmt4 -db ./db/test -dbtype prot -outfmt %f -out test.hits.2.fa


The file "fmt4" is like this :


Reference: Stephen F. Altschul, 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.
Reference for compositional score matrix adjustment: Stephen F.
Altschul, John C. Wootton, E. Michael Gertz, Richa Agarwala,
Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005)
"Protein database searches using compositionally adjusted
substitution matrices", FEBS J. 272:5101-5109.
Reference for composition-based statistics starting in round 2:
Alejandro A. Schaffer, L. Aravind, Thomas L. Madden, Sergei
Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and
Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST
protein database searches with composition-based statistics and
other refinements", Nucleic Acids Res. 29:2994-3005.

Database: db
           3 sequences; 498 total letters
Results from round 1
Query= T0658-D1
                                                                      Score     E

Sequences producing significant alignments:                          (Bits)  Value
2  unnamed protein product                                            342     5e-127
1  unnamed protein product                                            342     5e-127
0  unnamed protein product                                            342     5e-127





Lambda      K        H        a         alpha
   0.316    0.133    0.379    0.792     4.96


I am lost here. Could you give me some help? Great thanks in advance!

software error • 488 views
ADD COMMENTlink modified 19 months ago by lieven.sterck8.2k • written 19 months ago by ygxing10

Does fmt4 file have one input entry gi/Accession # per line?

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax87k

hi! Yes! there is. But I do not know how to post them clearly. Very sorry.

ADD REPLYlink written 19 months ago by ygxing10

It looks like your fmt4 file has actual blast results. You can use only accession numbers (One per line) with -entry_batch directive.

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax87k

Yes, this is a psiblast output file with "outfmt" equals 4. Do you know how to extract all the accession numbers from the output file?

There is a weird problem. I can extract the hits from some other fmt4 files. But I fail in some fmt4 files also.

comparing these fmt4 files carefully, I did not find any useful clues.

ADD REPLYlink written 19 months ago by ygxing10

You should have used a tabular format for the results. It looks like this is a custom database of some sort, correct? It may be easier to re-run the blast otherwise you are going to need to parse this file.

ADD REPLYlink written 19 months ago by genomax87k

Thank you very much! Yes, this is a custom database.

After one night enough sleep, I get your point.

ADD REPLYlink written 19 months ago by ygxing10
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