Question: finding novel protein
0
gravatar for saadleeshehreen
5 months ago by
saadleeshehreen40 wrote:

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.

genome • 208 views
ADD COMMENTlink modified 5 months ago by h.mon20k • written 5 months ago by saadleeshehreen40
1
gravatar for h.mon
5 months ago by
h.mon20k
Brazil
h.mon20k 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 5 months ago by h.mon20k

Thanks a lot . :) I will try Mauve

ADD REPLYlink written 5 months ago by saadleeshehreen40
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