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 (www.r-project.org) as well as the R package Biostrings (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.