How To Find Bacterial Genomes Lacking Certain Type Of Genes

Question

[Pappu]

I am searching for bacterial genomes which lack certain type of proteins which are probably essential for their function. The idea is to predict which sort of protein they have instead for that function. I have got sequences and HMMs of the proteins I am interested. I am wondering which tool would be suitable for this purpose.

Answer 1

[Istvan Albert]

Well download all bacterial genomes then use an aligner to find the protein. Use a cutoff to filter for genomes that don't have a protein of sufficient similarity.

[Pappu]

Thanks, I downloaded all bacterial genomes from ENA and wrote hundreds of lines of python code for analysis. How can I confirm that my scripts are working properly? Also I don't want to waste time reinventing the wheel.