pegi3s/blast repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of BLAST⁠, a program that finds regions of similarity between biological sequences. It compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

⁠Using BLAST image in Linux

In order to use this image you need to create a custom database from a multi-FASTA file of sequences with this command: docker run --rm -v /your/data/dir:/data pegi3s/blast makeblastdb -in /data/mydb.fasta -dbtype nucl -parse_seqids

See the following section, Building a BLAST database with local sequences⁠, for more details.

After the creation of the database, in order to execute a blastn for instance, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/blast blastn -query /data/input -db /data/mydb.fasta -evalue 0.05 -num_descriptions 500000 -num_alignments 500000 -outfmt 3 -out /data/output

In this command, you should replace:

• /your/data/dir to point to the directory that contains the query file you want to execute.
• input to the actual name of your query file.
• mydb.fasta to the actual name of the database you created.
• output to the actual name of your output file.

For other options common to all BLAST search applications please go here⁠.

Note: The parameter max_target_seqs does not behave as it is described. Please read the following article⁠.

To obtain abbreviated help of an application, you just need to run: docker run --rm pegi3s/blast <blast-application-name> -h (e.g. docker run --rm pegi3s/blast blastn -h). For more extensive documention just replace the -h flag for the -help flag.