Initial import of hmmer version 2.0.
Profile hidden Markov models for biological sequence analysis. PR: 7120 Submitted by: Matthew Jason Euclid Barnhart <barnhart@sequencer.wustl.edu>
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svn path=/head/; revision=11871
36
biology/hmmer/Makefile
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biology/hmmer/Makefile
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# New ports collection Makefile for: hmmer
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# Version required: 2.0
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# Date created: June 29 1998
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# Whom: barnhart@genetics.wustl.edu
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#
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# $Id$
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#
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DISTNAME= hmmer-2.0
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CATEGORIES= biology
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MASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/
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EXTRACT_SUFX= .tar.Z
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MAINTAINER= barnhart@genetics.wustl.edu
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BUILD_DEPENDS= perl:${PORTSDIR}/lang/perl5
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MAN1= hmmalign.1 hmmbuild.1 hmmcalibrate.1 hmmconvert.1 hmmemit.1 hmmer.1 hmmpfam.1 hmmsearch.1
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WRKSRC= ${WRKDIR}/build/${DISTNAME}
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post-build:
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@ strip ${WRKSRC}/binaries/*
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@ make test
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test:
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@(cd ${WRKSRC}; make test)
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post-install:
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.if !defined(NOPORTDOCS)
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${MKDIR} ${PREFIX}/share/doc/hmmer
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${INSTALL_MAN} ${WRKSRC}/Userguide/Userguide.ps ${PREFIX}/share/doc/hmmer
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.endif
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@ ${CAT} ${PKGDIR}/MESSAGE
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.include <bsd.port.mk>
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1
biology/hmmer/distinfo
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biology/hmmer/distinfo
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MD5 (hmmer-2.0.tar.Z) = 7e993a3883046840f0672ea004bc268b
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1
biology/hmmer/pkg-comment
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biology/hmmer/pkg-comment
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Profile hidden Markov models for biological sequence analysis.
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biology/hmmer/pkg-descr
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biology/hmmer/pkg-descr
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HMMER is an implementation of profile HMM methods for sensitive database
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searches using multiple sequence alignments as queries.
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Basically, you give HMMER a multiple sequence alignment as input; it builds
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a statistical model called a "hidden Markov model" which you can then use as
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a query into a sequence database to find (and/or align) additional
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homologues of the sequence family.
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Hmmer is developed by Sean Eddy at Washington University School of Medicine.
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More information is available at http://hmmer.wustl.edu/
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biology/hmmer/pkg-message
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biology/hmmer/pkg-message
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*********************************************************
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Note on environment variables:
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HMMER reads three environment variables:
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HMMERDB - directory location of HMM databases (e.g. PFAM)
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BLASTDB - directory location of FASTA-formatted sequence databases
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BLASTMAT - directory location of PAM scoring matrices
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If you have installed BLAST, you probably already have these
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environment variables set in system-wide or user-specific
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.cshrc files. They are optional. If they are set up, you
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can simplify command lines to:
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> hmmpfam pfam my.query
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> hmmsearch my.hmm swiss35
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instead of
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> hmmpfam /some/long/path/to/databases/pfam my.query
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> hmmsearch my.hmm /some/long/path/to/databases/swiss35
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Please see the website http://hmmer.wustl.edu/ for more information.
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*********************************************************
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biology/hmmer/pkg-plist
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biology/hmmer/pkg-plist
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bin/hmmalign
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bin/hmmbuild
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bin/hmmcalibrate
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bin/hmmconvert
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bin/hmmemit
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bin/hmmpfam
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bin/hmmsearch
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man/man1/hmmalign.1.gz
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man/man1/hmmbuild.1.gz
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man/man1/hmmcalibrate.1.gz
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man/man1/hmmconvert.1.gz
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man/man1/hmmemit.1.gz
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man/man1/hmmer.1.gz
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man/man1/hmmpfam.1.gz
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man/man1/hmmsearch.1.gz
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share/doc/hmmer/Userguide.ps
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