How To Extract Common Cds Among Huge Data Set?

Question

[HG]

Hi everyone, I have 50 Ecoli whole genome sequence data set. I already assemble all the genome. Next step i want to extract all the common CDs among all the 50 contig file in a batch mode. Can anyone please suggest me any approach?

[Pavel Senin]

as we discussed before, you can do prodigal and follow by cd-hit and counting in clusters

[HG]

Yes..its one good idea. In fact have started also. Let me compare others approach also. So that i can compare better result.

[HG]

Hi Pavel, After finding the gene and the traslated file how it is posiible to find funtion of each gene ...for example i need in a tabular format ....

Answer 1

[aawitney]

You could try annotating one of the genomes (I would use prokka http://www.vicbioinformatics.com/software.prokka.shtml). Then BLAST each of the annotated genes against all the other sets of contigs and list only the genes which have a significant hit in each genome,