tacg Version 2
a command-line program for the analysis of nucleic acids for unixy OSs.
tacg was originally designed for Restriction Enzyme analysis and it still
does so (better than ever), but it has also been expanded to more general
analyses, including:
o multiple degenerate pattern matching *with* errors,
o handling and matching degenerate input sequence,
o proximity matching of patterns (ie. report if siteA is < 200b from siteB)
o ORF analysis and
o export of data for use with external plotting/analysis tools
o more features, bug fixes, robustness.
o a whole new set of bugs ;)
If you are familiar with GCG's suite of programs, it includes much of the
functionality of MAP, MAPPLOT, TRANSLATE, and FINDPATTERNS, except that:
- it's cheaper (free* - Damn that asterisk!)
- it's faster (~2 - 15 times faster for most things)
- it does a few things that GCG doesn't do.
- it can parasitize NEdit (the excellent, free Xwin text editor) to become
a pretty slick (if simple) GUI biosequence application (and the just
released Nedit 5.0 gained an internal macro language, so further
integration will be forthcoming)
- most internals are dynamically allocated, so there are few limitations
on input sequence size, numbers of patterns to search for, etc.
- it runs (or will run) on more platforms, including/especially Linux
(Intel, Alpha, PPC), IRIX, SunOS, Solaris, HP UX/Exemplar OS, NeXT, DEC
Unix/OSF - anything for which there's a gcc or other ANSI C compiler)
- you can look at/scoff at/improve on the source code.
* in short, you can use the program and source code for anything you want
without charge, even in commercial ventures. The only thing you have to
contact me about is if you want to incorporate the program or it's source
into another program or package that you will sell for profit.
It's not a database scanner (yet - next order of business), but it will do
Megabase sequences quite handily.
Nuff said. If you're interested, read how to get it at:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg2.main.html
If you decide to use it, you might be interested in subscribing to the
(probably low-flow) tacg listserv to be notified of bugs found and
squashed, new features, suggestions, etc. The page above tells how.
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There's an HTML-ized man page at:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg2.man.html
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The original WWW interface is at:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.form.html
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and the mockup of the new one is at:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg2.form.html
The original WWW form interface to tacg should be running soon with the new
version of tacg underneath, for more robustness and some more features.
I'll post when it's set to go.
New WWW forms that take advantage of most of V2's features will come
online as time allows and interest demand, with one form dealing with
restriction enzyme analysis, another dealing with pattern and proximity
matching. Also, postscript conversion and in-line compression of returned
results are in the works for the new interfaces.
Cheers
Harry
--
Harry J Mangalam, MolBio+Biochem / Dev+Cell Bio, Rm 4201, BioSciII UC
Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598
