Script to find common/unique CDS between two genomes

[Dagga]

Hi All,

I was wondering if anyone could suggest a script that would allow me to comparatively analyse two genomes.

I was hoping I could use the gene (or protein) list of two organisms and input each list as a separate fasta file.

Then, the script would compare all of the CDS from each list and the output would be common (organisms 1), unique (organism 1), unique (organism 2) and contain in fasta each of the genes in fasta format.

cheers

[Thias]

Probably a flight of fancy, but you could get an idea by directly estimating abundances from k-mers of one transcriptome/genome, which you find back in the other.

I guess you will have to abuse some tools written for a different purpose, but those papers may still be useful:
Nordström et al. and Patro et al.

[biocomputer]

I haven't used this program but I came across it a while ago and it might help. I think you can get a free trial but have to pay after that.

http://www.bioinfor.com/ph/general/overview.html