WWWtacg Version 1.6 - Restriction Enzyme Analysis via the Web

Harry Mangalam mangalam at uci.edu
Tue Nov 12 17:55:43 EST 1996


    
 WWWtacg Version 1.6 - Restriction Enzyme Analysis via the Web

For those of you who have been requesting a Web-available resource for 
Restriction Enzyme 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 1.5 source code and executables for a variety of 
architectures:
ftp://mamba.bio.uci.edu/pub/tacg/

If you are especially 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.  tacgi lives at:

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

Note:  The currently available source code is for *Version 1.5*, not 
1.6, which I'm currently running thru testing and debugging on multiple 
systems.  Version 1.6 provides the features noted in the documentation and 
man pages.  The current snapshot of the source code for V1.6 is in the same 
distribution directory, but has only been tested on IRIX and Linux.


tacg provides many (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 'catalogs' (NEB, Promega, 
   Stratagene, Amersham, and one made up of only CHEAP enzymes) via
      Overhang generated (5', 3' or blunt)
      Magnitude of recognition sequence (4-cutters + up, 5-cutters + up, etc)
      Minimum and Maximum number of cuts
         or
   Direct specification via names (or, in the Web version, checkboxes from 
      a large list) (NEW)
      
   
Output in a variety of formats:   
   Linear map with *exact* cut site indicated
   Treat as linear or circular topology
   Translation with 1/3/6 frames in 1 or 3 letter codes
   Output width selectable from 60 to 230 characters
   GCG-type Ladder Map with 5' (\), 3'(/), and blunt (|) cutters indicated
   Pseudo Gel Map with 10 or 100 bp 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
- it runs on my system, not yours, therfore you don't have to install it 
   (although that'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


Bugs and Oddities:

Altho I didn't research it exhaustively when I started this, my impression 
was that Netscape was the only browser that supported file uploads, so this 
was writ and debugged with Netscape(2+3).  I have no great Browser 
preference (besides a philosophical opposition to things small and squishy, 
but Netscape allowed me to do what I wanted to do.  If Mosaic or IE now allow 
file uploads, so much the better.

Altho tacg supports sequence input into the millions of bases, the Web 
version supports an upload size of only 100,000 characters.  I figure if 
you routinely want to do analyses of >100Kb, you can download the program 
and run them on your own machine.

While the form allows upload of anything, unless the file is ASCII text, 
you may get odd or no results.  Binary file uploads are not supported, so 
don't expect intelligible results from from your MacVector or Lasergene 
files.

While the analysis times for 100,000 bases are relatively trivial (<5s, 
typically), the upload and especially download (up to 12x upload size) 
times can be significant .  If it's used enough and the output sizes are 
significant, I may add on-the-fly compression (output is especially 
well-suited to lzw compression).

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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