Similarly, a script was written to identify ion channels and GPCRs - genes that had a GO identifier for ion channel activity (GO 0005216) or G-protein coupled receptor activity (GO 0004930) or one of their more specific subterms (e.g., GO 0001584 rhodopsin-like receptor activity).
Koen (1985) wrote: "To identify a situation calling for an engineer, seek a situation calling for change".
In total, two different algorithms were specifically written as part of this study to divide the dataset into individual station-to-station profiles (extraction algorithms), and four different algorithms were written to identify the station pairs that each of these individual profiles corresponds to (classification algorithms).
Two Perl scripts were written to identify clusters of paralogous genes and subsequently calculate KS distributions.
A custom Perl script was written to identify those polymorphisms that were unique to the suppressor strain.
A PERL script was written to identify introns conserved in 2 or more species, defined as being within 10 amino acids in the multiple sequence alignment.
Perl scripts were written to identify and group the transcript-specific probes, create new CDF files and predict differentially regulated or detected transcripts.
On the basis of the algorithm by D'Antonio and Bagga [ 63], a program was written to identify the G-quartet motif in the NTs.
A Perl script was written to identify consecutive windows containing a minimum of ten unique piRNAs that held a single constraint.
Custom scripts (Additional file 3) were written to identify differences between the sequences of the strains, including single nucleotide polymorphisms and insertions and deletions, and to calculate protein percent identity, using the Mauve alignment as the input.
A custom python script was written to identify neighbour regulators, which we define as TF-encoding genes that regulate target genes which are encoded immediately adjacent on the chromosome.
