Run GPF

Description

Run GPF on de novo predicted peptides.

Input files

• exactly 1 GPF index file (.gpfindex)
• at least 1 GPF queries file (.fa | .faa | .fas | .fasta | .gpfqueries | .txt)

Output files

• GPF peptides (gpf-peptides.fasta)
• YAML results (gpf-results.yaml)
• CSV results (gpf-results.csv)

Context

Parameters

Masses

Choices: monoisotopic (default)

Similarity search

Choices: yes (default), no

Mass tolerance

Default: 700 ppm

Search introns

Choices: yes (default), no

Max intron length

Default: 2100 nucl.

Enzyme

Choices: Trypsin (default)

Minimum amino acid chain length

Default: 5

Source code

run-gpf.rb, run-gpf.yaml (GitHub)