Blast

#Introduction

Basic Local Alignment Search Tool (BLAST) is NCBI’s main tool for comparing a DNA or protein sequence with other sequences from various databases.

A BLAST search is one of the fundamental ways to learn about a protein or a gene: the search reveals which related sequences are present in the same organism and in other organisms.

#Blast+

The BLAST programs hosted on the NCBI website are extremely popular.

As an alternative, you can also use BLAST+, a set of command-line executables for local use. This alternative is very interesting, since it allows you to set up custom databases, perform massive searches (i.e., use a very large number of queries), implement complex search strategies through custom scripts, or use your computer cluster to improve performance.

At this link you have the manual: BLAST Command Line Applications User Manual.

#Working environment

To work with blast we will use the ncbi\blast image.

Download the script blast.sh:

$ wget https://gitlab.com/xtec/bio-blast/-/raw/main/blast.sh
$ chmod u+x blast.sh

Run the script - the first time it will take longer to run because it has to download the image:

$ ./blast.sh

...
Status: Downloaded newer image for ncbi/blast:latest
root@8e54f06bb10e:/blast#

The script also creates some shared folders between the container and your machine:

$ ls blast
...

To exit the container run exit:

$ exit