samkhn/pdb2fasta

Binary to convert a PDB formatted file and its protein data into a FASTA formatted file.

pdb2fasta

Author: Samiur Khan, [email protected]

Ackowledgements: Zhang Lab, Department of Computational Medicine and Bioinformatics at University of Michigan

Purpose

Binary to convert a PDB formatted file and its protein data into a FASTA formatted file. If the PDB file contains multiple amino acid chains, the resulting FASTA file will contain seperate chains split by the > character.

Installation

Clone the repository and, in your terminal, run

make main

This should create a pdb2fasta binary.

Usage

./pdb2fasta [path/to/pdb_file]

Running this will produce a fasta file with the name of the protein sequence.

For example, running

./pdb2fasta ./1tpo.pdb

will produce a 1tpo.fasta file. The fasta file will be stored in the same directory as the pdb file.

Assumptions about the PDB file

• The program assumes that the input PDB filename ends with ".pdb".
• The program assumes that, within the PDB file, the residue sequence identifier is an integer and that the residue chain identifier is a character.