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