new sites for web version of tacg

Harry Mangalam mangalam at home.com
Thu Sep 2 12:52:47 EST 1999


Hi All,

tacg is a command-line restriction mapping and pattern-matching tool that
runs on unixy systems (and has been ported in command-line mode to DOS,
Windows95/98/NT and even the Mac).
Version 3 will be forthcoming Real Soon Now.

However, this note is about public WWWtacg server availability.
The server that hosted the publicly available version of tacg at UC Irvine
crashed some time ago and was not restored.  A number of people have asked
about replacement servers so here are some that I know about:

http://24.1.175.29/tacg   
(this is the primary site - all new versions will be available here 1st)

http://darwin.bio.uci.edu/tacg

Catherine Letondal has also set up her own tacg interface at:
http://bioweb.pasteur.fr/seqanal/interfaces/tacg.html
which is a bit different than mine, but actually adds some more
functionality to it.


I'm compiling a list of alternative public servers to place on my web page
for when I release the beta of version 3 - I'm just finishing off the docs
and tacking on the last few functions which include:

- integration with Jim Knight's seqio (and therefore multiple sequence
    analysis as well as automatic reformatting), 
- matrix matching (using TRANSFAC-formatted matrices), 
- reverse translation (as part of 'Silent Sites', also new), 
- more protein info (est. pI, absolute and % composition of peptides)
- some elementary stats, 
- regular expression matching, 
- sliding window analysis  
- 'surrounding sequence' extraction, with auto rev. compl or not
- per-pattern min/Max filtering and logic (in a sliding window or not) 
- allows alternative pattern files for patterns, matrices, regular
    expressions, etc.
- lots of bug fixes, code cleanup, memory leak plugs, better formatting
- introduction of more bugs, but hopefully fewer than I fixed :)
- an example function to show how to explicitly add your own functions to
it
- autoconf configuration and 
- RPM packaging (mostly for Linux)

on top of the previous:

- Proximity matching, 
- searching with errors 
- 1|3|6 frame translations in 1|3 letter codes, using any Codon
    Translation table, ouput in FASTA format
- some primitive ORF finding (but not real gene finding yet), 
- degenerate (IUPAC) sequence handling in input sequence and patterns, 
- gel simulations (w/ hi/lo cutoffs), 
- ladder maps, 
- Linear maps, 
- tabular Sites, 
- multiply sorted tabular Fragments, 

written in ANSI C, w/ dynamic mem for most ops, developed on Lintel,
tested so far on SGI and Solaris; final targets are those and PPC Linux,
Alpha Linux, Compaq Tru64 (aka DEC Unix aka OSF), the BSDs, and maybe NT
and MacOS X.

The new WWW interface is also under development.  It will hopefully include
graphic plasmid map functionality.

-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 -- mangalam at home.com




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