gmap 2006.04.21 biology =0

A Genomic Mapping and Alignment Program for mRNA and EST Sequences
Maintained by: rpz@cse.wustl.edu
Port Added: 29 Sep 2006 05:09:50

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A standalone program for mapping and aligning cDNA sequences to a
genome. The program maps and aligns a single sequence with minimal
startup time and memory requirements, and provides fast batch
processing of large sequence sets. The program generates accurate
gene structures, even in the presence of substantial polymorphisms
and sequence errors, without using probabilistic splice site models.
Methodology underlying the program includes a minimal sampling
strategy for genomic mapping, oligomer chaining for approximate
alignment, sandwich DP for splice site detection, and microexon
identification with statistical significance testing.

WWW: http://www.gene.com/share/gmap

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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Required To Build: devel/gmake

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To install the port: cd /usr/ports/biology/gmap/ && make install clean
To add the package: pkg_add -r gmap

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Configuration Options

     No options to configure

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Master Sites:

http://www.gene.com/share/gmap/src/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

[patch] cleanup non-supported FreeBSD versions

PR:             ports/111727
Submitted by:   Edwin Groothuis <edwin@mavetju.org>
Approved by:    Bob Zimmermann <rpz@cse.wustl.edu>

Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA
and EST Sequences.

PR:             ports/103651
Submitted by:   Bob Zimmermann <rpz at cse.wustl.edu>

10 vulnerabilities affecting 29 ports have been reported in the past 14 days

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