On Thu, Apr 14, 2011 at 5:38 PM, Peter Cock wrote:
Hi all,
I just wanted to mention (to avoid duplicate work) that I have a working Galaxy wrapper for NLStradamus v1.6, a tool for prediction of nuclear localization signals (NLSs) from a protein FASTA file. The wrapper does a little reformatting of the output to get a clean tabular file for use in Galaxy.
I would release this to the Galaxy Tool Shed now, but the tool's author Alex Nguyen Ba tells me he hopes to have an update released fairly soon which should include a native tabular output - probably with a richer column structure. So rather than having to change the tool output and potentially break workflows, I plan to wait till then.
Alex has released NLStradamus v1.7 which includes built in support for tabular output (with scores added). This new release also includes both the original Perl implementation, and a new C++ implementation which is much faster. I have updated my wrapper and submitted it to the Galaxy Tool Shed, http://main.g2.bx.psu.edu/
References:
A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses. NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. BMC Bioinformatics. 2009 Jun 29;10(1):202.
Regards,
Peter