There, biologists of a coming generation will employ new tools for exploring the gene scripts that made the wonders of biological development and survival happen.
Dr. Brown's laboratory investigates the gene expression scripts of the yeast and human genomes - their organization, physiological logic and the molecular mechanisms that control them.
For the remaining genes a script implemented by us was used in order to identify the coding sequences beginning with a start codon and ending with a stop codon.
For the remaining genes a script implemented by us was used in order to identify the coding sequences beginning with a start codon and ending with a stop codon in order to calculate reliable GC, GC1, GC2 and GC3 values (the GC levels of first, second and third codon position).
Mechanosensitive endothelial gene expression profiles: scripts for the role of hemodynamics in atherogenesis?
Expression levels were estimated for all the Ensembl genes using Python script rpkmforgenes with parameters -readcount -no3utr [ 23], which ignores 3' UTRs.
For expressed genes with homology greater than 10e-6 to an Arabidopsis gene, custom perl scripts were written to parse and tally each transcript GO slim ID for biological process, molecular function, and cellular process.
To automatize motif discovery on the various non-coding sequence types for the different clusters defined during this study, we used the script gene-cluster-motifs, a task manager available in the stand-alone version of RSAT.
For each gene, custom PERL scripts assessed intron number and alternative splicing (i.e. the position or length of any alignable intron or internal exon is different in at least two different isoforms).
ZL performed the literature mining and candidate gene selection using scripts written by NT, binary filtering and prioritization of candidate genes, and protein-protein interaction and functional enrichment analysis; wrote some basic programs for database mining, assembled the set of candidate genes; contributed to the study design, and drafted the manuscript.
Each SNV was annotated with a custom-made Perl script and gene information available from WormBase v. WS220.
