====== HMMER ======

Biological sequence analysis using profile hidden Markov models
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  * Install

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<code>
cd /root/
wget ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/hmmer-3.1b1-linux-intel-x86_64.tar.gz
tar -xvzf hmmer-3.1b1-linux-intel-x86_64.tar.gz
cd hmmer-3.1b1-linux-intel-x86_64/
./configure
make
make check
make install

cd /db
wget ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
gunzip Pfam-A.hmm.gz
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  * Test

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<code>
hmmalign -h
# hmmalign :: align sequences to a profile HMM
# HMMER 3.1b1 (May 2013); http://hmmer.org/
# Copyright (C) 2013 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Usage: hmmalign [-options] <hmmfile> <seqfile>

Basic options:
  -h     : show brief help on version and usage
  -o <f> : output alignment to file <f>, not stdout

Less common options:
  --mapali <f>    : include alignment in file <f> (same ali that HMM came from)
  --trim          : trim terminal tails of nonaligned residues from alignment
  --amino         : assert <seqfile>, <hmmfile> both protein: no autodetection
  --dna           : assert <seqfile>, <hmmfile> both DNA: no autodetection
  --rna           : assert <seqfile>, <hmmfile> both RNA: no autodetection
  --informat <s>  : assert <seqfile> is in format <s>: no autodetection
  --outformat <s> : output alignment in format <s>  [Stockholm]

Sequence input formats include:   FASTA, EMBL, GenBank, UniProt
Alignment output formats include: Stockholm, Pfam, A2M, PSIBLAST

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