BLAST+ Subtractive genomics

Question

[daniellaplummer1993]

Hello

Can anyone explain how I would find the essential genes in C. difficile by using standalone BLAST+, also if it is then possible to subtract these from the human genome using BLAST+.

Thanks

Answer 1

[Siva]

Conserved genes (or core genes) in two species from distant lineages can be considered as essential genes. You can use COG database, which includes your species of interest, to identify such core genes.. Look for COGs that have broad phyletic distribution (e.g. includes species from Firmicutes and Proteobacteria) and get the protein GIs of C. difficile from those COGs.

With the GIs, you can get the protein sequences and then do a BLAST search against human proteins.