SignalP results - extract full sequence for proteins with a signal peptide

Question

[JMac]

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?

Answer 1

[dago]

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