WWWtacg - Restriction Enzyme Analysis via the Web

Harry Mangalam mangalam at uci.edu
Wed Oct 16 14:55:53 EST 1996


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 'tacg', my freely available, command-line restriction enzyme 
analysis tool for unixy systems:

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

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

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

A preview of the Restriction Enzyme selection form that should be rolled 
into the code Real Soon Now:
http://hornet.bio.uci.edu/~hjm/projects/tacg/rebase.select.html

The FTP site for the source code, and executables for a variety of 
architectures:
ftp://mamba.bio.uci.edu/pub/tacg/

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 via:
   Overhang generated (5', 3' or blunt)
   Magnitude of recognition sequence (4-cutters + up, 5-cutters + up, etc)
   Minimum and Maximum number of cuts
   
Output in a variety of formats:   
   Linear map with *exact* cut site indicated
   Treat as linear or circular 
   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
- 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, the 
upload and especially download times can be significant (up to 12x input 
size).  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).

Special Thanks go to Fred Criscuolo for the 1st iteration of the Web form 
and Tom Boutell for his V1.1 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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