Can I use dCNS to identify CNS and PAV in one species

baoxingsong / dCNS

conserved non-coding sequence

MIT License

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Can I use dCNS to identify CNS and PAV in one species #24

Open shangguandong1996 opened 2 years ago

shangguandong1996 commented 2 years ago

Hi, Dr song I want to see whether flanking sequence of genes in one gene family have CNS and "PAV", so I am wondering whether I can identify CNS in one species to set query and ref as same species.

Best wishes

Guandong Shang

baoxingsong commented 1 year ago

As far as I know, you need to have enough phylogenetic distance to identify CNS, no matter which software you would like to use. For closely related genomes, there may be not enough time to generate enough genomic variants to separate negatively selected elements from neutrally selected elements.