Updated user guide

I’ve added some sections to the version of the HMMER User’s Guide that’s linked at hmmer.org. You can download the new Guide from here.

The Guide now briefly describes the HMMER3 acceleration pipeline for profile/sequence comparison, and the methods used to identify domain “envelopes”, maximum expected accuracy alignments, and posterior probabilities of aligned residue confidence. The Guide also now documents the --tblout and --domtblout tabular output formats.

This should help address questions about what all the fiddly columns mean in these outputs, especially in --tblout.

This version of the Guide included in HMMER distro tarballs is still the old version. The updated Guide will appear in distro tarballs for 3.1, which is coming Real Soon Now.

2 thoughts on “Updated user guide

  1. hello sir,
    I want to know can I build a database of many .HMM files so that I can directly search my all genomic CDSs in a go with that database. If yes, how can i do this?
    Thanks in anticipation.

    Like

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s