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Old 01-19-2008, 02:20 AM
Charles Plessy
 
Default Bug#461504: ITP: tacg -- command line program for finding patterns in nucleic acids

Package: wnpp
Severity: wishlist
Owner: Charles Plessy <charles-debian-nospam@plessy.org>

Package name : tacg
Version : 4.1.0
Upstream Author : Harry Mangalam, tacg Informatics
URL : http://sourceforge.net/projects/tacg
License : GPL and others
Programming Lang: C (tacg), Perl (CGI)
Description : command line program for finding patterns in nucleic acids

tacg is a character-based, command line tool for unix-like operating systems
for pattern-matching in nucleic acids and performing some of the basic protein
manipulations. It was originally designed for restriction enzyme analysis of
DNA, but has been extended to other types of matching. It now handles
degenerate sequence input in a variety of matching approaches, as well as
patterns with errors, regular expressions and TRANSFAC-formatted matrices.
.
It was designed to be a grep for DNA and like the original grep, its
capabilities have grown so that now the author has to keep calling up the help
page to figure out which flags (now ~50) mean what. tacg is NOT a GUI
application in any sense. However, it's existance as a strictly command-line
tool lends itself well to Webification and wrapping by various GUI tools and
it is now distributed with a web interface form and a Perl CGI handler.
Additionally, it can easily be integrated into editors that support shell
commands such as nedit.
.
The use of tacg may be cited as: Mangalam, HJ. (2002) tacg, a grep for DNA.
BMC Bioinformatics. 3:8 http://www.biomedcentral.com/1471-2105/3/8

I had to apply an ugly patch in order to compile it with gcc4. Because I am not
a C programmer, I barely understand what I did, so I would appreciate comments
on the patch:

http://svn.debian.org/wsvn/debian-med/trunk/packages/tacg/trunk/debian/patches/to-build-with-gcc4.patch?op=file&rev=0&sc=0

This is a low-quality patch, but it works. The modificaiton of tacg.h was
made according to what I found on the mailing lists, and seems to make
sense. The modification of SeqFuncs.c is completely heuristic; I used the
same numbers as in tacg.h. The modification of SetFlags.c is a quick
workaround that does not solve the real problem.

Also, you can consult the full copyright file in the same repository:

http://svn.debian.org/wsvn/debian-med/trunk/packages/tacg/trunk/debian/copyright?op=file&rev=0&sc=0

I use tacg to search for oligonucleotides in sequence reads: I need to allow
mismatches, and want to detect if I (unfortunatley) cloned concatemer
artefacts. If you know a better tool, let me know !

Have a nice day,

--
Charles Plessy
Debian-Med packaging team
Wakō, Saitama, Japan
 

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