tacg Central

Docs & Resources

tacg is a command-line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms a core of the program, it has been expanded to fill more roles, sort of a 'grep' for DNA. However, it is also more than that: a brief description of its abilities is at the bottom of this page.

The lines below will become linked-in as the backing fuctionality comes online.

Download the tacg source code
- from author's private stock
- from SourceForge
Check out the Sourceforge tacg dev site.
Check out the bleeding edge CVS version.

List of some active WWWtacg servers *

Author's dev machine (slow, but latest) Stable UNstable

UC Irvine Stable UNstable

Cal State Fullerton Stable UNstable

* Let me know if you install a tacg server and want it listed here.

New features visible in the UNstable Web versions include:

analyzing sequence retrieved by accession # from NCBI (Web version only)
creating circular Postscript or PDF plasmid maps with degeneracies plotted around the circumference and any/all ORFs plotted as well. Click on the image to the left panel for a PDF example.

What tacg is:

It is a command-line tool, albeit one designed for humans. It has compiled-in brief help hints, a decent man page (and expanded version thereof in the HTML version) and an [in-progress] full length manual as well.
It was written congruent to the philosophy that most large-scale bioinfomatics will done in a pipeline and therefore the tools for those analyses should support pipelines as much as possible. Ideally such a tool should be designed so that you can pour in a megabytes of data and the pipeline will return you the 7 bytes that really interest you. The underlying algorithms should be fast enough that you can work interatively, adjusting parameters and re-running the analysis until it's perfect. tacg is not there yet, but that's the goal.
It is also written with the philosophy that relatively small, efficient tools are often more effectively used than large 'frameworks' writ by committee intent on standardizing the universe. If the tool develops a following, then the user community (rather than a committee) drives the development of new options, standardized interfaces, etc. Small tools tend to be more easily understood by those that might contribute to them, and while C is an old, grunty language, it's small, fast, well-understood (except for pointers and memory allocation), has universal compiler support via gcc, and there is a vast support structure and code base for it.
tacg is also highly applicable to Web interfaces and an updated one will be made available shortly to replace the one based on the older version 2 (still running HERE). The base code is included in the distribution, but is not well described or formatted for easy installation.
It was intended and written for the analysis of genomic DNA, so it uses dynamic memory for almost all internal storage and therefore it is not limited to a specific sequence length.
It is written in ANSI C, using standard libaries or supplied code, so that it compiles and runs on all unix variants that I've tried: Linux (PPC, Intel, Alpha (64-bit)), DEC Unix(64bit), IRIX(32/64bit), Solaris, ConvexOS, HP/UX, NeXTStep. It also runs on Win95/NT (compiled with the amazing Cygwin tools), DOS (with the DJGPP extender), and has been compiled for the Mac as part of Don Gilbert's SeqPup application, although the DOS and Mac versions have not yet been compiled for recent versions.
It is meant to be extended to include your own functions. An example skeleton function is included as a guide, so that even relative newbie programmers should be able to plug in analytical code to extend it.

It supports: [* = new or improved in version 4]

* Circular Plasmid maps in postscript or PDF, with degeneracies marked and ORFs from any/all frames plotted as well.
* cloning support (search for enz's that do/don't cut in specific ranges
searching arbitrarily large nucleic acid strings (dynamic memory allows searching whole bacterial genomes, or eukaryotic chromosomes (or genomes) in one sweep)
handles sequences as small as 5 bases for analysis of linkers, oligos
handles circular and linear DNA appropriately, correctly
allows subsequences to be extracted from larger sequences, generates both subsequence #ing and original sequence #ing
can also number the sequence arbitrarily, including negative start points
integrated with Jim Knight's Seqio to allow automatic sequence conversion on input, and scanning multiple sequence databases
fast (5-35X equiv routines in GCG and EMBOSS) pattern matching of nucleic acids up to about 50 base patterns.
simultaneous searching of thousands of patterns read from a database or a few explicit patterns read from the command-line
searching with errors (mismatches, not indels, tho that's coming soon).
searching for patterns containing IUPAC degeneracies in strings which also contain IUPAC degeneracies
searching for regular expressions (in nucleic acid), with autoconversion of IUPAC degeneracies to the appro regex.
searching for TRANSFAC matrices, with user-specified cutoffs.
GCG-style ladder maps.
gel simulations with low and high end cutoffs for 'zoomable' views of the gel
selection of Restriction Enzymes explicitly, by overhang generated, magnitude of recognition site, enzyme price, minimum, maximum number of cuts (overall or on a per-pattern basis)
supports Combination Cuts of up to 15 REs at a time
supports limited AFLP fragment matching / simulation
simulates Dam and/or Dcm methylation of DNA
generates summaries of # of patterns found, Sites, Fragments (sorted/unsorted)
searches for silent sites, with reverse translation
Full Linear Maps with enzyme cuts marked AT THE POINT OF CUTTING, not beginning of pattern, with 1/2 strands, optional tics for very compact display
co-translation of DNA, based on a (user-expandable) number of Codon usage tables, in 1/3/6 frames, with 1 or 3 letter AA labels
* ORF finding in any combination of frames (1/2/6 for example) with FASTA output, with offsets in DNA, protein, Molecular Wt, pI, with optional additional info on AA frequency in #s or %
dump of internal data for analysis / plotting with external plotting programs in 3 formats, incl gnuplot.
* conditional output based on matches, for scanning large numbers of sequences at a time
* 2 types of Proximity matching:
1. exact specification of the relationships of 2 patterns (upstream, downstream, by how much, within/outside of a range
2. specify rules for arbitrarily complex relationships among many patterns (in a sliding window or in the whole sequence) with logical AND, OR, XOR conjunctions joining pattern specifications (editorial comment: this is cool)
  for example: (((A AND B) OR (C XOR D) OR E) AND (F AND G))
  Rules once typed and verified are logged to a file so they can be incorporated into a file of rules (see below)
* Now supports FILES of Rules, so you can make up a file of Rules that you're interested in & search for them all at once, without the horrible typing each time.
sequence extraction surrounding pattern matches, with variable upstream, downstream inclusion, optional reverse translation in FASTA format.
* uses autoconf/configure to ease building on different platforms.
* includes an explicit example function to show how to add your own funtionality
Dual Licensed - GPL or Proprietary Use.
Source code included, of course!