BLAST demonstration: makeblastdb, blastn, tblastn

by rnnh 4 years ago

GNU/Linux ◆ xterm-256color ◆ bash 1220 views

This is a demonstration of some of the tools in the NCBI BLAST+ suite.

In this demonstration, makeblastdb is used to create a BLAST database from the file S_cere_genomes.fna. This FASTA nucleic acids (.fna) file was created by concatenating the following Saccharomyces cerevisiae genome assemblies, which were downloaded from NCBI: GCA_003086655.1, GCA_003709285.1 and GCA_004328465.1.

The program blastn is then used to query 23S_rRNA_gene.fna against this database. This file is a copy of the Scutellospora fulgida isolate NC303A 25S ribosomal RNA gene from NCBI.

The program tblastn is also used to query YPK1.faa against this database multiple times. This FASTA amino acid (.faa) file is a copy of the serine/threonine-protein kinase YPK1 from UniProt. This search is carried out multiple times with additional parameters: the flag -evalueis used to set an E-value threshold, and the flag -max_hsps is used to set a maximum number of High-scoring Segment Pairs (HSPs).

The results from these BLAST searches are written to tab-separated values (.tsv) files. This output format is specified with the flag -outfmt 6.

Copy of the conda environment used during this video demonstration.

Made for https://rnnh.github.io/bioinfo-notebook/.

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