stand alone psi-blast

Question

[crystalrose]

I'm using psi-blast (blast version 2.2.30+),this is my command:

psiblast -query seq.fasta -db db -num_threads 15 -out outfile.txt -outfmt 6

I'm not sure than if I have got the right result.It seems that it only run one iteration. But if I add the parameter: -num_interations 2, warnings appear:

Frequency ratios for PSSM are all zeros, frequency ratios for BLOSUM62 will be used during traceback in composition based statistics

I don't know where is the mistake and how can PSSM are all zeros. any help will be appreciated!

[1992minto]

hi ! here , I get the two matrix of PSSM , but I don't their meaning .As shown in the follow picture

[Ram]

You have broken links. Please open a new question and add a link to this question in there so people can help you out.

Answer 1

[Ram]

PSSM scores might be all zeros because no domains were found in the input sequences. Could you give us more details on how the db was created?

[crystalrose]

Thanks for your answer.I create the db using my own fasta file:makeblastdb -in seq.fasta -dbtype prot -out db -parse_seqids.The fasta file here is the same as psiblast query file.I want to classify these protein seqeuences ,which can't be classified into pfam ,by psiblast.

[Ram]

Are you sure running PSI-BLAST against the same set of sequences as both subject and query is a good idea? What is your ultimate aim?

[crystalrose]

Actually, I aim to classify protein families for some protein sequences.I think I should change my strategy and search the known-function-sequence db. Do you think this can be work?

[Ram]

You might wanna just query against nr or SwissProt. Classification is usually done by checking homology to proteins with known function. If your query is all unknowns and you're not looking to internally cluster them, the DB should be nr or SwissProt.

[crystalrose]

Thanks for your help!I sovled this problem by adding an parameter -comp_based_stats 0 and got some conserved results.