PILOT IMPLEMENTATION of Translated (protein-to-DNA) search in a HMMER fork

IF YOU ARE LOOKING FOR OUR TRANSLATED SEARCH SOFTWARE, PLEASE VISIT THE BATH REPOSITORY: https://github.com/TravisWheelerLab/BATH

---

DEPRECATED DESCRIPTION BELOW

WARNING: This is a fork of the HMMER repository, and should not be treated as the original.

HMMER searches biological sequence databases for homologous sequences, using either single sequences or multiple sequence alignments as queries. HMMER implements a technology called "profile hidden Markov models" (profile HMMs).

This fork includes a new tool, hmmsearcht, for performing so-called "translated search", directly comparing a file of protein profile HMMs to a target set of one or more nucleotide sequences. Other standard HMMER tools are not compiled, to avoid clashing with a standard hHMMER installation.

The approach is functionally equivalent to identifying all open reading frames (ORFs) in the target sequence, then searching them with hmmsearch. These two new tools contribution (hmmsearcht) provides a few benefits; most importantly:

• it simplifies the process of parsing results to recover hit positions
• it presents alignments showing both amino acid and encoding codons

to clone a copy of this fork of HMMER3 source from github:

   % git clone https://github.com/TravisWheelerLab/trans-hmmer 
   % cd hmmer
   % git submodule init
   % git submodule update --remote
   % autoconf
   % ./configure
   % make

You will find the executables hmmsearcht and hmmscant in the src/ directory, along with a copy of hmmbuild.

to report a problem:

Visit the main HMMER repo issues tracking page at github.