Peptide design and oligonucleotide encoding

This website provides usage information for a variety of scripts that were written to aid in the design of synthetic oligonucleotides for use in PepSeq library synthesis. Example files for running commands have been supplied for each script, and a full length tutorial walking through the full process from starting dataset of full length proteins to a final library of DNA oligonucleotides encoding that can be used to create a full library of PepSeq probes.

The modules described here include:

One Hundred Reps - A script used to reduce the size of your target protein sequence file by removing identical protein sequences.

Sliding Window - Runs a sliding window approach to tile across input proteins sequences to create peptides of user defined size.

Set Cover - Runs a set cover algorithm to design peptides for a given protein sequence fasta file, or a directory of protein sequence fasta files.

SW-SC - Runs a set cover algorithm to design peptides for a given protein sequence fasta file, or a directory of protein sequence fasta files.

Oligo Encoding - Script that can be used generate nucleotide encoding for all designed peptides

Tutorial - A full tutorial walking through the steps to design a library of unique peptides for all of the proteins assigned to the Poxviridae family downloaded from UniProt.

Click on the links above for descriptions of the individual scripts and associated tutorials.