Question: predicted protein and sequence
0
gravatar for mdfardin374
9 months ago by
mdfardin37410
mdfardin37410 wrote:

Hello, I am interested in fetching all the predicted protein (proteins that do not have experimental evidence) of a particular organism or hypothetical proteins of an organism so that MS/MS analysis can be carried out to prove proteomic evidence. Can somebody please help me?

sequence • 275 views
ADD COMMENTlink modified 9 months ago by genomax91k • written 9 months ago by mdfardin37410
1
gravatar for fishgolden
9 months ago by
fishgolden450
fishgolden450 wrote:

I use uniprot for such purpose.

It has PE line. https://www.uniprot.org/docs/userman.htm#PE_line

Check an example. https://www.uniprot.org/uniprot/Q8YW84.txt

ADD COMMENTlink written 9 months ago by fishgolden450
0
gravatar for genomax
9 months ago by
genomax91k
United States
genomax91k wrote:

Using EntrezDirect. This example uses Malus as an example.

$ esearch -db protein -query "MALUS DOMESTICA [ORGN]" | esummary | xtract -pattern DocumentSummary -element Caption | grep "^XP" | xargs -n 1 sh -c 'efetch -db protein -id "$0" -format fasta'
ADD COMMENTlink modified 9 months ago • written 9 months ago by genomax91k
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