iTAK is a bioinformatics software tool for easy and logical identificatoin of plant trasnscription factors and transcription domains as defined by Lehti-Shiu MD, Shiu S-H (2012). iTAK utilizes both plnTFDB and plantTFBD as referance databases
Read the paper and cite the paper t http://authors.elsevier.com/sd/article/S1674205216302234
If you're running linux, iTAK has a very simple setup. The only outside requirnments are an up to date installation of BioPerl. iTAK comes with a precompiled version of hmm.
If you're not using linux, then a custom installation of hmm will need to be done, and a copy of all binaries will need to be placed in the /bin folder of iTAK
To download iTAK you cna either download it from our website ftp://bioinfo.bti.cornell.edu/pub/program/itak/old or clone this github repo using
github clone https://github.com/kentnf/iTAK.git
Once bioperl is installed you can test your installation of iTAK by running
perl iTAK.pl test_seq
iTAK is a relativly simple program to call
Example:
perl iTAK.pl Multifasta -o ItakOutput
Parameters:
-f [String] Frame used for nucleotide translation.
6: 6 frame translation (default)
3F: 3 frame translation with forward strand
3R: 3 frame translation with reverse strand
-a [Integer] Number of CPUs used for hmmscan (default = 1)
-o [String] Name of the output directory (default = "input file name" + "_output")
The Output from iTAK will be a list of files
tf_sequence.fasta: sequences of all identified TFs/TRs (FASTA format).
tf_classification.txt: classification of all identified TFs/TRs. A tab-delimited txt file containing sequence IDs and their families.
tf_alignment.txt: A tab-delimited txt file containing alignments of all identified TFs/TRs to the protein domain database.
pk_sequence.fasta: sequences of all identified PKs (FASTA format).
Shiu_classification.txt: classification of all identified protein kinases. A tab-delimited txt file containing sequence IDs and their corresponding protein kinase families.
Shiu_alignment.txt: A tab-delimited txt file containing alignments of all identified protein kinases to the protein domain database.
- Issue Tracker: github.com/iTAK/iTAK/issues
- Source Code: github.com/iTAK/iTAK
If you are having issues, please let us know. Contact us at http://bioinfo.bti.cornell.edu/cgi-bin/itak/contact.cgi
The project is licensed under the BSD license.