Bioinformatics Programming

A collection of articles on bioinformatics programming published in Bioinformatics Review.

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Latest Bioinformatics Programming News

Extracting first and last residue from helix file in DSSP format.

Previously, we have provided a tutorial on using dssp_parser to extract all…

Dr. Muniba Faiza Dr. Muniba Faiza

How to extract x,y,z coordinates of atoms from PDB file?

The x, y, and z coordinates of atoms are provided in the…

Tariq Abdullah Tariq Abdullah

dssp_parser: A new Python package to extract helices from DSSP files.

A new Python package named 'dssp_parser' is developed to parse DSSP files.…

Dr. Muniba Faiza Dr. Muniba Faiza

How to calculate center of mass of a protein structure using Python script?

Here is a Python script that helps you calculate the center of…

Dr. Muniba Faiza Dr. Muniba Faiza

How to sort binding affinities based on a cutoff using vs_analysis.py script?

Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual…

Dr. Muniba Faiza Dr. Muniba Faiza

Installing Pycharm on Ubuntu (Linux)

Pycharm is an integrated development environment (IDE) for developers. It combines Python…

Tariq Abdullah Tariq Abdullah

vs_Analysis.py: A Python Script to Analyze Virtual Screening Results of Autodock Vina

The output files obtained as a result of virtual screening (VS) using…

Dr. Muniba Faiza Dr. Muniba Faiza

How to execute Unix/shell commands in PHP?

Besides, Python & Perl, PHP is another language mostly used in bioinformatics…

Dr. Muniba Faiza Dr. Muniba Faiza

How to search for a specific character in a file using Python?

In this article, a simple python script is provided that can be…

Dr. Muniba Faiza Dr. Muniba Faiza

Nested SQL queries and aggregate functions for complex information retrieval from a database

In one of our previous articles, we have mentioned a few basic…

Dr. Muniba Faiza Dr. Muniba Faiza

Basic SQL Queries to Create and Retrieve Information from a Database

In this article, basic SQL queries are described to create, update, drop,…

Dr. Muniba Faiza Dr. Muniba Faiza

Some common awk bash commands to modify multi-FASTA files

Some basic operations on multi-FASTA sequence files is a tedious task without…

Dr. Muniba Faiza Dr. Muniba Faiza

Extract FASTA sequences based on sequence length using Perl

Here are simple Perl scripts to filter out FASTA sequences from a…

Dr. Muniba Faiza Dr. Muniba Faiza

Operations on FASTA files using Perl, PHP, and Bash commands

We have published various articles on bioinformatics programming dealing with large files…

Tariq Abdullah Tariq Abdullah

Modifying multi-FASTA files using Bash: ‘Sed’ Command

Dealing with thousands of FASTA sequences is a tedious task without using…

Tariq Abdullah Tariq Abdullah

Perl script to find duplicate FASTA sequences using their header?

In a large file of FASTA sequences, it is nearly impossible to…

Dr. Muniba Faiza Dr. Muniba Faiza

How to perform graph-based clustering of peptide/protein sequences using MCL?

Markov Cluster Algorithm (MCL) is a clustering algorithm that clusters networks .…

Tariq Abdullah Tariq Abdullah

How to concatenate FASTA sequences using Perl?

Here is a simple Perl script to concatenate multiline FASTA sequences into…

Dr. Muniba Faiza Dr. Muniba Faiza

How to search motif pattern in FASTA sequences using Perl hash?

Here is a simple Perl script to search for motif patterns in…

Dr. Muniba Faiza Dr. Muniba Faiza