Question: SignalP results - extract full sequence for proteins with a signal peptide
0
gravatar for JMac
2.6 years ago by
JMac20
Ireland
JMac20 wrote:

I am using the program SignalP (v4.1) to predict if proteins are secreted.

Using the parameter '-m' generates a FASTA file containing the predicted signal peptide sequences.

Is there any option to quickly generate a FASTA file containing the entire sequence of proteins containing signal peptides?

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by JMac20
2
gravatar for dago
2.6 years ago by
dago2.5k
Germany
dago2.5k wrote:

take the ID of the proteins, for example:

cat results_here | grep ">" > Ids_of_positive_proteins

and then use pyfaidx as explained by Matt Shirley here:

A: extract sequences from multi fasta using partial ID

The original multifasta would be the file where you have the complete sequences and the query is the Ids_of_positive_proteins

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by dago2.5k
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