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Bioinformatics Programming

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

Tariq Abdullah

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operations on fasta

We have published various articles on bioinformatics programming dealing with large files consisting of multiple FASTA sequences. Here is a list of articles related to operations on multi-FASTA files using Perl, PHP, and some bash commands.

How to read fasta sequences as hash using perl?

This is a simple Perl script to read a multifasta file as a hash. Keep reading

A perl script to convert multiline FASTA sequences into a single line

There are different software or tools which require different kinds of input, especially, when you are trying to developing a pipeline or want to process multiple large files. If you are dealing with a big FASTA file consisting of thousands of sequences split into a particular number of residues per line, and you want each sequence into a single line, then you can use this simple Perl program. Keep reading

How to read fasta sequences from a file using PHP?

Here is a simple function in PHP to read fasta sequences from a file. Keep reading

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

Here is a simple Perl script to search for motif patterns in a large FASTA file with multiple sequences. Keep reading

How to concatenate FASTA sequences using Perl?

Here is a simple Perl script to concatenate multiline FASTA sequences into a single line. The script provided in this article can also be used for large files consisting of multiple FASTA sequences split into the indefinite number of residues per line. Keep reading

Perl script to find duplicate FASTA sequences using their header?

In a large file of FASTA sequences, it is nearly impossible to perform some operations manually. This is a simple Perl script to find out duplicate sequences in a multi-fasta file using a FASTA header. Keep reading

How to extract fasta sequences from a multi-fasta file based on matching headers in a separate file?

This is a simple Perl script to extract FASTA sequences from a large fasta file depending on the matching fasta headers present in another file. Keep reading

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

Dealing with thousands of FASTA sequences is a tedious task without using bioinformatics programming. It eases multiple minute tasks to be performed on FASTA sequences or their headers such as removal, addition, or substitution of certain characters in the header, or manipulating the sequence format, and so on. In such cases, shell bash commands provide an easy way to perform such tasks on FASTA sequences. Keep reading

Linux ‘sed’ command in Perl programming

When it comes to handling large data files to process, it becomes very difficult to write programs for the beginners, especially when you have to execute another script within one. For this purpose, the Linux operating system offers several advantages for bioinformatics programming such as ‘awk’ and ‘sed’ one-liners, they prove to be of great help! Keep reading

How to execute Unix/shell commands in a Perl script?

BioPerl is a collection of Perl modules that are used to write Perl scripts applied in bioinformatics [1]. It is used in bioinformatics programmings such as in developing source codes, standalone software/tools, and algorithms. It’s easy to install and provide various modules which make it easier to execute different functions. However, Python is mostly preferred over the Perl language, still, some of the bioinformatics software is based on Perl such as the standalone version of I-TASSER. Sometimes, it’s a big trouble to execute some Unix/shell commands in Perl script for the beginners, it’s difficult to decide which function would be specific to a condition. Therefore, this article is a guide for the execution of Unix/shell commands in Perl script. Keep reading

Perl one-liners for bioinformaticians

Perl one-liners are extremely short Perl scripts written in the form of a string of commands that fits onto one line. That would amount to a bit less than 80 symbols for most purposes. Here’s the obligatory “Hello World!” one-liner in Perl and it’s output: Keep reading

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

Bioinformatics Programming

sminalog_analysis.py – A new Python script to fetch top binding affinities from SMINA log file

Dr. Muniba Faiza

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sminalog_analysis.py – A new Python script to fetch top binding affinities from SMINA log file

In one of our previous posts, we provided a Python script for the virtual screening analysis of Autodock Vina. This script analyzes all log files obtained from docking of multiple ligands to a receptor and provides the binding affinities for top poses from each file. In this article, we are publishing a new Python script for the virtual screening analysis of SMINA [1]. (more…)

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Bioinformatics Programming

Installing Pycharm on Ubuntu (Linux)

Tariq Abdullah

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Installing pycharm on Ubuntu

Pycharm [1] is an integrated development environment (IDE) for developers. It combines Python developer tools and provides an easy graphical user interface. In this article, we are going to install Pycharm on Ubuntu. (more…)

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Algorithms

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

Dr. Muniba Faiza

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VS-Analysis: A Python Script to Analyze Virtual Screening Results of Autodock Vina

The output files obtained as a result of virtual screening (VS) using Autodock Vina may be large in number. It is difficult or quite impossible to analyze them manually. Therefore, we are providing a Python script to fetch top results (i.e., compounds showing low binding affinities). (more…)

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