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tacg / WWWtacg (1.7) Restriction Enzyme Analysis Programs

Harry Mangalam mangalam at uci.edu
Mon Dec 23 17:03:19 EST 1996


New releases of tacg and WWWtacg:

      WWWtacg Ver 1.7 - Restriction Enzyme Analysis via the Web
     and tacg Ver 1.7 - A command line program for unixy systems
     
For those of you who have been requesting a Web-available resource for 
Restriction Enzyme (and now Transcription Factor) analysis and mapping, 
here are the URLs for the WWW interface to the latest version of 'tacg', my 
freely available, command-line restriction enzyme analysis tool for unixy 
systems:

The form for submitting sequence and specifying output:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.form.html

The page describing the program in detail:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.main.html

The HTML-ized man page:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.man.html

The FTP site for the Version *1.7* source code and executables for a variety of 
architectures, currently:

              Hardware                  Operating System
              DEC Alpha                 OSF1 3.2
              SGI (all architectures)   IRIX 5.3
              SPARC                     SunOS 4.1.3
              UltraSPARC                SunOS 5.5
              Intel [3456]86            Linux 2.0.0 (elf)

ftp://mamba.bio.uci.edu/pub/tacg/


If you are especially security-minded or simply masochistic, you can 
download and install both the WWW form and docs, the cgi interface program 
(called tacgi) and the tacg program itself.  I've only tested it on Linux 
and SGI's so you're on your own for the Web version on other platforms, 
although it also compiles on a variety of Suns.  

The tacgi package lives at:
ftp://mamba.bio.uci.edu/pub/tacg/tacgi


Version 1.7 adds:

- User definable sorting: Either you can have the Sites and Fragment 
   tables, Gel simulations, and Ladder Map output printed in the same 
   sequence as the RE names appear in the Database file (alphabetically) or you 
   can have them sorted by # of hits/cuts, and thence alphabetically.  The 
   latter is very much like DNA Strider's output.  The previously available 
   sorting of Fragments, by sequence, by size or both is still available.  
   To my surprise, even tho the sort is not at all elegant, it adds no 
   detectable run time to the program.
   
- tacg now handles a compact version of the Transcription Factor Database 
   (TFD), allowing you to map all of the ~2000 TFs in that database as you 
   would Restriction Enzymes.  This is a crude (but still useful?)  version 
   of the work in progress that will handle arbitrary numbers of errors, 
   regular expressions insertions and deletions, proximity filters, using 
   tacg's compact output format.
   The Web version allows you to select it as one of the databases; the 
   database itself is available at the main FTP site above and is bundled 
   with the executables and source code, with the other alternative REBASEs.


General Overview:

tacg provides most of the features of the GCG 'MAP' program and a 
few more (including a much better linear format, IMHO).

Enzyme selection by:

   Indirect specification from several different supplied 'catalogs':
         REBASE
         NEB 
         Promega 
         Stratagene 
         Amersham 
         only CHEAP enzymes (>$40U/$) 
         Transcription Factor Database (aka TFD) *NEW* 
         
   via:
      Overhang generated (5', 3' or blunt)
      Magnitude of recognition sequence (4-cutters + up, 5-cutters + up, etc)
      Minimum and Maximum number of hits
         or by
         
   Direct specification via names (or, in the Web version, checkboxes from 
      a large list)
      
   
Output in a variety of formats:   
   Linear map with *exact* cut site indicated
   Treat as linear or circular topology
   Subsequences allowed (numbered relative to both parent and subsequence)
   Translation with 1/3/6 frames in 1 or 3 letter codes
   Output width selectable from 60 to 230 characters
   Tabular Output now sortable by # cuts as well as alphabetically *NEW*
      (this sorting affects all the options below tagged with '^')
   GCG-type Ladder Map with 5' (\), 3'(/), and blunt (|) cutters indicated^
   Pseudo Gel Map with 10 or 100 bp low end cutoff^
   Table of Cut Sites^
   Table of Fragments (Sorted, Unsorted, or both)^
   Summary Table of Cuts
   Strider-like linear summary of infrequent cutters


The WWW interface provides access to all the functions (except the 
subsequence selection) of the original program and a few extras:

- an HTML/Forms-based pseudo GUI (definitely works with Netscape; others 
   not tested extensively)
- File browser for large sequence uploads, so you don't have to deal with 
   repeated 'cut+pastes'.
- it runs on my system, not yours, therefore you don't have to install it 
   (although it's pretty easy..)
- because of the above, it obviously works with Macs and PCs, as well as 
    anything else that runs a web browser.
- the hyperlinked help and online man page.
- hyperlinked Table of Contents of the results built on the fly
- 3 selectable font sizes (but viewing depends on your browser)
- a few different header sizes for distinctive results separators


For Bugs and Oddities, see the home page noted above.

Thanks to Fred Criscuolo for the 1st iteration of the Web form and Tom 
Boutell for his V1.10 cgic library.

Hope it's of some use,
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



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