Package: wnpp Severity: wishlist Owner: Charles Plessy <[EMAIL PROTECTED]>
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 WakÅ, Saitama, Japan
