Make Blast Database

Introduction

The makeblastdb application, provided by NCBI, produces BLAST databases from FASTA files. It is possible to use completely unstructured FASTA files, but this is not the recommended procedure. Assigning a unique identifier to every sequence in the database allows retrieving the sequence by identifier and also associating every sequence with a taxonomic node (through the taxid of the sequence).

Please cite Make Blast Database: https://www.ncbi.nlm.nih.gov/books/NBK569841/

OmicsBox offers the possibility to build a Blast database with your own sequences.

Run Make Blast Database

This functionality can be found under functional analysis → Blast → Make Blast Database. This option allows creating a BLAST database from the sequence of any OmicsBox project or from a FASTA file (figure 1).

Configuration

The Make Blast Database Configuration require the following parameters.

  • Current project: OmicsBox will use the loaded sequences to create the Blast database. Note: If the resulting database will be used for further GO mapping a proper ID and description line with "GO mappable'' information are needed.

  • FASTA file: This option allows choosing own FASTA file. The FASTA file has to be correctly formatted for NCBI Blast+.

  • Output Folder: Select the directory where to save the created Blast database.

  • Blast Database Name: Provide a name for the Blast database

  • Taxonomy Options:

    • Taxonomy ID: Introduce the NCBI species ID

    • Mapping file: If the sequences come from different species, it is possible to generate a text file with the sequence names and its species id to map to the corresponding sequence in the FASTA file. 

    • Example:

    • TR|A0A022PMT6|ERYGU	4155
      TR|A0A022PMU0|ERYGU	4155
      TR|A0A059BJ72|EUCGR	71139
      TR|A0A059BJ72|EUCGR	71139
      TR|A0A061FDU3|THECC	3641
      TR|A0A067DJ79|CITSI	2711

Visit the following tutorial for more information on how to create the Taxonomy ID file.

Figure 1: Make Blast Database

Results

Once the execution has finished the Blast database folder contains all the files needed to run Local Blast.