secmarker 0.4.1

secmarker description

secmarker

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. Old version was written in python2 and now it's written in python3

SECMARKER 0.4

• 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