hmmsearch force results for all query sequences

[gillichu]

I'm currently trying to get hmmsearch to give me bitscores for all my provided query sequences. I'm working with Pfam protein datasets. I've used the '--max' flag, but some sequences are still getting filtered out in the last domain-filtering step after the MSV, Viterbi and bias composition filters are turned off. Any advice to make bitscores for the query sequence names listed in missing_seq.txt show up in the hmmsearch output (searchout.txt) would be very helpful. I've attached files to reproduce this problem of missing sequences, as well as the relevant commands and versions I used.

Versions:

• HMMER 3.1b.2
• Pfam 34.0
• CentOS Linux 7 (Core)

My commands are:

hmmbuild --amino --cpu 5 PF00207.24.myhmm train_seq.txt
hmmsearch --noali --cpu 5 -o searchout.txt --max PF00207.24.myhmm test_queries.txt

Contents of example.zip:

• missing_seq.txt
• PF00207.24.myhmm
• searchout.txt
• test_queries.txt
• testseq_names.txt
• train_seq.txt

[cryptogenomicon]

I'm sorry, there is no way to do this in hmmsearch, by design. It is designed to identify the most significant hits, not to score all sequences.

[gillichu]

I see, thanks for your response!