SW-SC

Overview

The SW-SC script uses a combined sliding window/set cover algorithm to design peptides for a given protein sequence fasta file, or a directory of protein sequence fasta files.

Inputs

The only required input is a fasta-formatted file containing a set of target protein sequences.

Outputs

There is one required output, a fasta-formatted file containing the peptide sequences.

There is one optional output, a tab-delimited summary file, which shows the number of peptides designed for each input file (one line per input file).

Installation

• Because Python is an interpreted language, there is no installation required for the Python version of this script. The only requirement is Python 3.

Use

In this example, our input directory will contain ten files of aligned clusters created from a downsampled set of proteins from Poxviridae. (see full tutorial for creation of these files)

The outputshould contain ten files with 30 amino acid long peptides tiling across the input sequences along with a summary file showing the number of peptides designed for each cluster file. The ten peptide containing fasta files can then be concatenated into a single fasta file.

Command:

SW_SC.py \
  -u  /clusters/id_70_SW_SC_w30_s22_x9_sumStats.tsv \
  -s 22 \
  -x 9 \
  -y 30  \
  clusters/*