Category: Bioinformatics

This page contains short Bioinformatics tutorials. However, very informative on the basics needs for someone learning the topic, and tricks for someone more experienced. The posts target bioinformatics with python, definition, jobs, sequencing, metagenomics analysis, samtools, etc.

Bioinformatics

Creating a Multiple Sequence Alignment (MSA) Aware of Forward and Reverse Complement Directions – Easy

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This blog post teaches an easy way how to create a multiple sequence alignment (MSA) aware of forward and reverse complement directions.

BioinformaticsUnix

How to Create a RamDisk on Linux – Step-by-Step

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This tutorial will teach you how to create a ram disk on a Linux distribution and unmount it when needed. This lesson can be used to …

Bioinformatics

Calculate DNA Melting Temperature in Python – Step-by-Step

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This tutorial shows how to calculate DNA melting temperature (Tm) in Python using Biopython, installed using bioconda.

Bioinformatics

Masking Low Complexity Regions – Step-by-Step

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This tutorial teaches how to mask low complexity regions in a FASTA file using BBMap.

Bioinformatics

Fast FASTA/FASTQ Random Subsampling

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This short tutorial teaches how to subsample a paired FASTQ, single FASTQ, pair FASTA, or single FASTA file to a specific number of reads. This can …

Bioinformatics

Easy NCBI Genome Download

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NCBI genome download can be a very unpleasant job. This page shows how to use NCBI-genome-download to download NCBI genomes with a single command line easily.

Bioinformatics

Fast Conversion of Lowercase Sequences to Uppercase in FASTA Format

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This tutorial teaches two approaches to convert lowercase to uppercase sequences in FASTA format. In bioinformatics, a FASTA with lowercase bases implies that regions are low …

Bioinformatics

Quick Sequencing Depth and Coverage Check

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This tutorial teaches how to run a quick sequencing depth and coverage check for one or more reference sequences.

Bioinformatics

The Fastest Way to Read a FASTA in Python

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This tutorial teaches a fast approach to how to read sequences from large FASTA files in Python using Pysam. I know how reading large FASTA files …

Bioinformatics

Multiple Sequence Alignment – Theory and Practice – Step-by-Step

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This blog post described Multiple Sequence Alignment (MSA) focusing on the theory and practice – Step-by-Step using MAFFT and Muscle.