Question: Genomics, Proteomics, Transcriptomics, bacteria
0
gravatar for abdulsaboor131990
2.0 years ago by
abdulsaboor1319900 wrote:

Hello I have proteomic data of bacteria in FASTA form taken at stationary and exponential growth phase of bacteria in the presence and absence of end product. I want to identify key proteins that are responsible for tolerance to the end product of this bacteria. My questions are 1) how can I compare these fasta files (any tool or method) to identify the expressed proteins at exponential growth phase in the presence and absence of end product? 2) How can I identify the potential protein that are responsible for tolerance to the end products?

sequence genome gene • 370 views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by abdulsaboor1319900
1

I have proteomic data of bacteria in FASTA form

Can you elaborate how you got this data?
I'm not sure of which assay fasta is the output.

And please select a more meaningful title for your question(s) and select appropriate tags.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by WouterDeCoster43k

For your transcriptomic FASTA data, do the following:

  1. Use Rockhopper to de novo assemble the transcriptomes and compare one condition versus the other
  2. Use blastx to infer functionality of the differentially expressed transcripts from point 1
ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Kevin Blighe54k

Even though the title has everything in it, the only real data mentioned in the post is proteomic. It may be in the form of short peptides in fasta format.

ADD REPLYlink written 2.0 years ago by genomax78k

Yes, but could be interesting to know if it's a quantitative assay to do differential expression analysis.

ADD REPLYlink written 2.0 years ago by WouterDeCoster43k
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