NCBI tools in Linux

how to run several NCBI tools in the Linux environment

Students will learn how to use tools at the NCBI database in Linux

NCBI blast tools

Clustalw

SRA tools

some Biopython

pr3

GeoR

basic knowledge of Linux programming and molecular biology

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, pr design by pr3, or ing 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 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!

biology and bioinformatics students




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