HMMER

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HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.

Contents

[edit] Installing on Linux

[edit] Installing HMMER itself

$ apt-cache search hmmer
$ apt-get install hmmer

You have now installed 9 programs into /usr/bin/*hmm*.

Note (below) that apt-get doesn't install a bunch of demo files that are useful to see if the programs are actually functional or not, so below we grab the source code distribution too.

[edit] Installing the "EMBASSY" (EMBOSS) wrapper

List of programs. 

$ ln -s /usr/local/include /usr/local/share/EMBOSS/include

Now, you may proceed: 

$ cd src
$ wget ftp://emboss.open-bio.org/pub/EMBOSS/HMMER-2.3.2.tar.gz
$ tar xvzf HMMER-2.3.2.tar.gz
$ cd HMMER-2.3.2
$ ./configure --prefix=/usr/local/share/EMBOSS
$ make
$ make install
$ cp emboss_acd/ehmm* /usr/local/share/EMBOSS/acd/

You have now successfully installed a dozen or so programs here: /usr/local/share/EMBOSS/bin/*hmm*.

[edit] Verifying Install

To do a test run, the HMMER source code (not just the apt-get install above) is useful. So lets grab a source code distribution into /tmp just to use weeviterbi_test files therein to verify that everything is working: 

$ cd /tmp
$ wget ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-2.3.2.tar.gz
$ tar -xzvf hmmer-2.3.2.tar.gz
$ /usr/local/share/EMBOSS/bin/ehmmalign
  Align sequences to an HMM profile
  HMMER hidden markov model file: /tmp/hmmer-2.3.2/testsuite/weeviterbi_test.hmm
  Input protein sequence set: /tmp/hmmer-2.3.2/testsuite/weeviterbi_test.seq
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