NCBI Tools in Linux

person icon Matthew Cserhati

NCBI Tools in Linux

how to run several NCBI tools in the Linux environment

updated on icon Updated on Sep, 2023

language icon Language - English

person icon Matthew Cserhati

architecture icon Linux,Development,Programming Languages


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Course Description

Bioinformatics has become an entirely independent discipline. This branch of science can greatly speed up and facilitate biological and biomedical research. As a biology or medical student or researcher you might be using bioinformatics tools at NCBI. You might also be interested in learning how to use these programs in Linux to make your work more efficient by automating them. This course helps you do exactly this.

In this course we will learn how to use the Linux version of several NCBI tools, such as ClustalW, bl2seq, analyzing GEO data sets, primer design by primer3, or downloading sequences using a Biopython script. We will also learn how to format BLAST databases and run Blast queries against them. We will also learn about the SRA database and how to download SRA NextGen fastq data sets.

In order to take this course some knowledge of Linux is required. For example we will write a shell script and a python script in one of the videos. You also have to know how to navigate in a Linux environment and run commands, but it should not be too difficult.

I hope that the knowledge that you gain in this course will help you become a more effective researcher.

Have fun!

Who this course is for:

  • biology and bioinformatics students


What will you learn in this course:

  • NGS

  • NCBI blast tools

  • Clustalw

  • SRA tools

  • some Biopython

  • primer3

  • GeoR


What are the prerequisites for this course?

  • basic knowledge of Linux programming and molecular biology

NCBI Tools in Linux


Check out the detailed breakdown of what’s inside the course

1 Lectures
  • play icon Introduction to the course 03:19 03:19
3 Lectures
4 Lectures
3 Lectures
SRA tools
2 Lectures
Primer design with primer3
2 Lectures

Instructor Details

Matthew Cserhati

Matthew Cserhati

bioinformatics; sequence analysis; Next Generation Sequencing

PhD in bioinformatics and BSc in software development from the University of Szeged. 20 years programming experience, 10 years experience in Nextgen sequencing. Associate level certification in Python at the Python Institute. Knowledge of Linux, R, MySQL, C, PHP, Perl.

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