## SECMARKER 0.4

Secmarker is a search tool for selenocysteine tRNA (tRNA-Sec) identification.
The presence of tRNA-Sec in a genome indicates the use of selenocysteine by the organism.

* Web server
  A SecMarker web server is available for online analysis:
  http://secmarker.crg.es/

* Publication
 Didac Santesmasses, Marco Mariotti and Roderic Guigó. Computational identification of the selenocysteine tRNA (tRNASec) in genomes. PLoS Comput Biol. 2017 Feb 13;13(2):e1005383. doi: 10.1371/journal.pcbi.1005383. 

* Dependencies
  cmsearch and esl-sfetch from the Infernal package (http://infernal.janelia.org/), specifically, version => 1.1 is required.
  RNAplot from ViennaRNA package (http://www.tbi.univie.ac.at/RNA/), version >= 2.0 is known to work fine.

* Installation:
  In order to use Secmarker run the following comands (where x.x corresponds to the current version):

  tar xfz secmarker-x.x.tar.gz
  cd secmarker-x.x
  ./setup.py
  ./run_test.py


* Running Secmarker.py
usage: Secmarker.py [-h] -t TARGET [-o O] [-plot] [-T T] [-F F] [-cpu CPU]
                    [-cca] [-AT12] [-O O]

search for selenocysteine tRNA (tRNA-Sec), marker of Sec trait

optional arguments:
  -h, --help            show this help message and exit
  -t TARGET, --target TARGET
                        target nucleotide sequence
  -o O                  output folder
  -plot                 generate the tRNA plot(s). For each tRNA prediction,
                        two files (.png and .ps) will be generated in the
                        folder images/
  -T T, --infernal_score T
                        score threshold used by cmsearch (Infernal score)
  -F F, --filtering_score F
                        score threshold used to filter tRNAs. If the tRNA has
                        the UCA anticodon or a G73, -T is used for filtering
  -cpu CPU              number of available CPUs [default 1]
  -cca                  include the 3 residues downstream the discriminator
                        base if available (to check if the CCA sequence is
                        encoded in the sequence)
  -AT12                 force a 12 bp AT-stem, that is a 7/5 fold tRNA
  -O O, --options O     additional options for cmsearch




* Contact us:
  [email protected]


Roderic Guigó lab
Centre for Genomic Regulation (CRG), Barcelona
2015-2020