Description
In the article listed below, we characterized the detailed binding specificity
of the RNA binding protein GLD-1 which is specifically expressed in the C.elegans
germline. We incorporated these binding determinants into a small R script which
can be used to scan any given sequence for GLD-1 binding motifs (GBM’s). To make
use of the software, install R (http://www.r-project.org) as well as the R package
Biostrings (http://www.bioconductor.org). Download and extract the GBM finder
(zip file listed below) into an empty directory and start R. Execute the example
script example.r that scans the test sequences provided in seqs.fa by typing
source('example.r').
The function which performs the scan (scanForGBMs) is called as follows:
hits <- scanForGBMs("seqs.fa","GBM_scores.tab")
where seqs.fa is the fasta file with the sequences that should be scanned and
GBM_scores.tab is the table which contains the search parameters (provided in
the zip file). The result of the scan is returned in the table hits.
Download GBM finder
Citation
A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1.
Jane E Wright, Dimos Gaidatzis, Mathias Senften, Brian M Farley, Eric Westhof, Sean P Ryder and Rafal Ciosk
EMBO Journal 2010; doi:10.1038/emboj.2010.334