Question: finding novel protein
gravatar for saadleeshehreen
4 weeks ago by
saadleeshehreen30 wrote:


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.

genome • 115 views
ADD COMMENTlink modified 4 weeks ago by h.mon15k • written 4 weeks ago by saadleeshehreen30
gravatar for h.mon
4 weeks ago by
h.mon15k wrote:

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.

ADD COMMENTlink written 4 weeks ago by h.mon15k

Thanks a lot . :) I will try Mauve

ADD REPLYlink written 4 weeks ago by saadleeshehreen30
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