Top hit from phmmer
0
2
Entering edit mode
5.6 years ago
Morgan S. ▴ 90

Hey guys,

I have googled this and can not find any advice or answer. Hopefully, I have not overlooked it. I need phmmer to only write the top hit for each query I provide. Currently, it provides over a 100 hits for almost every query, which I have 12,000 of. It would take me way too much time to sort through all this information. Is it probably best to just use Blast instead where I can set this threshold? Not sure if it matters, but I set the evalue to 1e-3.

Thanks!

hmmer phmmer gene annotation genome • 2.2k views
ADD COMMENT
0
Entering edit mode

Are you just looking for the longest substring in the sequence on each iteration?

ADD REPLY
2
Entering edit mode

I don't think I understand your question. I used a protein fasta file made up of all the predicted genes in my genome. When I searched it against the MEROPS database, it gave me over 100 matches for each gene. I only want phmmer to give me the top hit from the MEROPS database, based on the evalue, for each gene, is there a way to do this? I thought --domZ would do the trick, but it didn't. In the manual it says --domZ : Assert that the total number of targets in your searches is <x>, for the purposes of per-domain conditional E-value calculations, rather than the number of targets that passed the reporting thresholds. Here is my script.

phmmer --tblout 1368D_merops2.txt --cpu 20 --domZ 1 -E 1e-3 /query/ /database/
ADD REPLY
0
Entering edit mode

Has anybody figured out an answer to this yet? I am looking for PHMMer equivalent of -max_target_seqs from BLAST.

max_target_seqs  
Number of aligned sequences to keep.   
Use with report formats that do not have separate definition line and alignment sections such as tabular (all outfmt > 4).   
Not compatible with num_descriptions or num_alignments. Ties are broken by order of sequences in the database.
ADD REPLY

Login before adding your answer.

Traffic: 1339 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6