HMMER
Biological sequence analysis using profile hidden Markov models
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
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 |