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gmap

spliced and SNP-tolerant alignment for mRNA and short reads

Variants:
This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of * known splice sites and identify novel splice sites. * known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA.
Homepage:
Package version:2012-06-12-1
Architecture:amd64
Distribution:Debian
Filename:gmap_2012-06-12-1_amd64.deb

/usr/share/doc/gmap/README.Debian

Prebuilt genome databases for GMAP and GSNAP are available from the
GMAP web site:
http://research-pub.gene.com/gmap/

 -- Shaun Jackman <sjackman@debian.org>  2010-04-28

/usr/share/doc/gmap/README.gz

0.  Availability
============

The source code for this package is available from
http://research-pub.gene.com/gmap.  License terms are provided in the
COPYING file.


1.  Building and installing GMAP and GSNAP
==========================================

Prerequisites: a Unix system (including Cygwin on Windows), a C
compiler, and Perl

Step 1: Set your site-specific variables by editing the file
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/usr/share/man/man1/gmap.1.gz

GMAP(1)                     User Commands                    GMAP(1)



NAME
       gmap - Genomic Mapping and Alignment Program

SYNOPSIS
       gmap -dDB|-gFASTA [OPTION]... [QUERY]...

DESCRIPTION
       Align the sequences QUERY to the reference, specified with -d
       or -g.  With no QUERY, read standard input.

OPTIONS
   Input options
       -D, --dir=directory
              Genome direct
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/usr/share/man/man1/gmap_setup.1.gz

GMAP_SETUP(1)               User Commands              GMAP_SETUP(1)



NAME
       gmap_setup - cre
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/usr/share/man/man1/gsnap.1.gz

GSNAP(1)                    User Commands                   GSNAP(1)



NAME
       gsnap - Genomic 
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/usr/share/doc/gmap/changelog.Debian.gz

gmap (2012-06-12-1) unstable; urgency=low

  * New upstream release

 -- Shaun Jackman <sjackman@deb
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/usr/share/doc/gmap/changelog.gz

2012-06-12  twu

    * VERSION, trunk: Updated version

    * Makefile.gsnaptoo.am: Removed extra in
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/usr/share/doc/gmap/copyright

Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: GMAP
Upstre
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