CNS Discovery Pipeline
The CNS Discovery Pipeline is a suite of software developed within the Freeling lab to identify orthologs or homeologs and compare the regions surrounding the genes to identify regions of noncoding DNA which have retained greater than expected sequence similarity, indicating the sequences (conserved noncoding sequences or CNS) are under functional constraint.
The CNS Discovery Pipeline was originally created by Brent Pedersen. His version of the software avaliable on github.
Ongoing development of the CNS Discovery Pipeline in now handled by Gina Turco. Download the latest version of the source code here
Example
The above example compares the coding sequence surrounding two homeologs from [Plant paleopolyploidy#2 Arabidopsis alpha|the Arabidopsis alpha tetraploidy] AT1G03170 and AT4G02810. Manually identified CNS based on blast searchers are marked below the dotted line in teal and CNS identified above the dotted line are drawn above the dotted line in purple. This example analysis can be regenerated using this link: http://genomevolution.org/r/4bpo
Publications Utilizing the CNS Discovery Pipeline
May be out of date.
- Woodhouse, M.R. et al. (2010). Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLoS Biol 8: e1000409.
- Schnable, J.C. et al. (2011). Dose-sensitivity, conserved noncoding sequences and duplicate gene retention through multiple tetraploidies in the grasses. Front. Plant Sci. 2:2.