hmm search target sequences
Hello,
I am trying to annotate fasta protein sequences in the Pfam database. I only want to get the best hit for each of my sequences. How can I do this with hmmsearch or phmmer?
Thank you
• 2,112 views
•
link
updated
by
Ram
•
written
by
emertekin •
•
written
by
emertekin •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Pfam database score filtering
written by ijarne •
-
Identifying very closely related proteins
written by Baby Bioinformatician
-
Make a multiple sequence alignment with a HMMER hmmsearch output?
written by westin.kosater •
-
BLAST multiple database against each other
written by archana.bioinfo87
-
Downloading all Helix-turn-helix motif containing protein from bacteria
written by saadleeshehreen
-
get domains of proteins
written by emanismail.92 •
-
How to integrate interproscan results into a fasta file
written by kamel •
-
Batch retrival of fasta sequences based on pfam (interpro) identifier
written by rzaja •
-
HMMER: Failed to open target sequence database for reading
written by Cayro •
-
Reciprocal best hit by blast
written by qwzhang0601
Is there a specific reason why you don't want to use the pfamscan.pl script provided on the pfam site? As far as I remember, it returns the best hit with default settings and it generally works quite well.