remove-signal-peptides

Remove signal peptides

Remove signal peptides from a UniProt fasta database.

Installation

1. Ensure GO is installed.

2. Clone repo

git clone https://github.com/gingraslab/remove-signal-peptides.git
cd remove-signal-peptides

1. Build executable

go build

Requirements

1. UniProt database in fasta format. These can be downloaded by searching, for example, for reviewed human entries and downloading in fasta format

https://www.uniprot.org/uniprotkb?facets=model_organism%3A9606%2Creviewed%3Atrue&query=%2A

1. List of signal peptides.

The list of signal peptides can be generated at UniProt with the following search:

https://www.uniprot.org/uniprotkb?query=(ft_signal:*)

and then filtering by other criteria such as species, reviewed, etc. For reviewed human sequences, the url would be

https://www.uniprot.org/uniprotkb?facets=model_organism%3A9606%2Creviewed%3Atrue&query=%28ft_signal%3A%2A%29

And finally add a column to the results table for signal peptides. Click the Customize columns button above the table and look under PTM/Processing. Then download all results as a tab-separated (TSV) file. Ensure the Signal peptide column is the seventh column in the download file.

Run

1. Specify input files in main.go

2. Build

go build

1. Run

./remove-signal-peptides

1. Output: ./files/mature-sequences.txt