New version of tacg, a restriction enzyme mapping tool for unix

Harry Mangalam mangalam at uci.edu
Sat Sep 28 00:40:13 EST 1996


tacg, a program for the restriction enzyme analysis of DNA. << Release 1.5 >>
by Harry Mangalam, UC Irvine (mangalam at uci.edu, 714 824 4824)

tacg is a character-based, command line tool for the restriction enzyme 
analysis of DNA for unix-like operating systems.  

Briefly, it takes sequence from stdin, strips out anything not an 'a', 'c', 
't', or 'g', filters the resulting sequence thru the restriction enzyme 
database to generate the restriction sites and then does some basic 
calculations on that data to generate enzyme cut-frequency summary tables, 
tables of site and fragment data, a linear map (with or without 
translations), pseudo-graphical ladder and summary maps as well as gel 
simulations (using a simple log fit).  Enzymes can be filtered by a variety 
of criteria; these affect what is printed as output.

For the impatient, here's how one might use it:

tail +44 seq.file | tacg -n6  -o5  -F2  -l -g10 -L -w90 >seq.file.map

Translation: chop off the top 44 lines of seq.file (tail +44 seq.file) and 
pipe (|) the resulting sequence to tacg, returning info on all 6+ cutters 
(-n6) that generate 5' overlaps (-o5), giving me the sorted fragment sizes 
of those enz's that match (-F2) and both ladder (-l) and gel (-g10) map, 
along with the default linear restriction map (-L) and 1 letter, 1 frame 
translation (the default) and write the output 90 characters wide (-w90) to 
a file called seq.file.map

A longer version of this document, examples of output, binaries, and source code
are at:
                ftp://mamba.bio.uci.edu/pub/tacg/


Binaries have been compiled on and are available for a variety of 
Unix-related Operating Systems:

   Silicon Graphics/IRIX 5.3 (R3000, R4X00)
   Sun SPARC/SunOS (5.3, 4.1.3)
   DEC Alpha/DEC Unix aka OSF/1 (V3.0/347)
   DECStations (MIPS R3000-based)/Ultrix (4.2)
   Convex C3480/ConvexOS
   NeXT boxes (Black)/NeXTSTEP (3.2) 
   Intel PCs/Linux (1.2.8(486), 2.0.0 (586))

Source code has been uploaded to Don Gilbert's IUBIO archive and should 
eventually come to rest at:
ftp://ftp.bio.indiana.edu/molbio/restrict-enz/tacg-1.5-src.tar.gz

as well as Sunsite's Linux archive:
<ftp://sunsite.unc.edu/pub/Linux/apps/biology/tacg-1.5.tar.gz>
(latter also contains the Linux binaries)

Both executables and the ANSI C source code are freely available for 
nonprofit purposes. 

I'd also be interested in hearing suggested refinements and critiques.

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




More information about the Bio-soft mailing list