SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to cluster sequences using HMMER? Loczi94 Bioinformatics 4 12-30-2017 11:18 AM
Biopython blast parsing skbrimer Bioinformatics 5 12-11-2014 09:57 AM
Compare 10000 sequences in hmmer thh32 Bioinformatics 0 10-20-2014 07:56 AM
Parsing reads from SAM/BAM by orientation winsettz Bioinformatics 2 09-19-2013 05:16 PM
hmmer and pfam rhinoceros Bioinformatics 2 06-11-2013 04:44 AM

Reply
 
Thread Tools
Old 06-28-2019, 11:51 AM   #1
maxbio
Junior Member
 
Location: Amherst

Join Date: Jun 2019
Posts: 2
Default Parsing HMMER Reads in Biopython

Hello all,

I have obtained HMMER reads on 60 metatranscriptomic sequences, against Pfam, dbCAN2, and MEROPS databases. I ran the protein sequences through hmmsearch and now want to parse them for analysis in R. I want to use Biopythons SearchIO to do this since it has a parser for HMMER reads (HMMERIO) but the instructions on the Biopython wiki are very unclear as to how to do this. Does anyone have experience parsing HMMER outputs in Biopython?

Thank you very much.
maxbio is offline   Reply With Quote
Reply

Tags
bioperl, biopython, hmmer, hmmsearch, metatranscriptome

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:14 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO