finding novel protein

Question

[saadleeshehreen]

Hi,

I am interested to find protein X in bacteria A. We hypothesized some of the strains of bacteria A have protein X, while others haven't. We also assume protein X is missing within species of this particular genus A. I have downloaded the protein sequences of bacteria A from NCBI. Now, I want to compare the genomes to find out which proteins are missing/present in particular strains/species to find out my novel protein. How can I do that? Please suggest me a methodology/software for this particular analysis.

Answer 1

[h.mon]

Mauve can read genbank files as input, you can align the genomes and the output window will delimit the genes - it will be able to see missing / extra genes.

Or download the predicted proteins for each genome and use OMA or PorthoMCL to infer orthologous genes.

Finally, you may check if the work has already been done for you: search OMA, OrthoDB or eggNOG databases, among others.

[saadleeshehreen]

Thanks a lot . :) I will try Mauve