BLAST Service

Overview

The PATRIC BLAST service integrates the BLAST (Basic Local Aligment Search Tool) algorithms to perform searches against against public or private genomes in PATRIC or other reference databases using a DNA or protein sequence and find matching genomes, genes, RNAs, or proteins.

Using the BLAST Service

The BLAST submenu option under the Services main menu (Genomics category) opens the BLAST input form (shown below). Note: The BLAST Service can be used without logging in, but if you want to include your private genome in the BLAST results, you must be logged into PATRIC.

BLAST Menu

Options

BLAST Input Form

Sequence: This is the entry box for either the nucleotide or amino acid target search sequence. Cut-and-paste is supported.

Program: Depending upon the type of sequence (nucleotide or amino acid) entered into the Sequence text box sequence, this will open a dropdown box showing the types of BLAST available. These include the following:

  • blastn: searches nucleotide databases using a nucleotide query
  • blastx: searches protein databases using a translated nucleotide query
  • tblastx: searches translated nucleotide databases using a translated nucleotide query
  • blastp: searches protein databases using a protein query
  • tblastn: searches translated nucleotide subjects using a protein query

Database: Dropdown list of a variety of PATRIC databases or user-selected data sets for searching. Depending upon the query type, searches are available for entire genomes or limited to only features. Specifically, blastn, tblastn, or tblastx, allows searches against either genomes or features. However, blastp or blastx are limited to features (proteins) only.

Advanced Options

BLAST Parameters: Allows adjustment of maximum number of hits returned and E value threshold.

Buttons

Search: Launches the search which, upon completion, returns a set of results matching the sequence provided and selected criteria. On the results page, the Edit form and resubmit Button above the search results reloads the input form so that the parameters can be easily adjusted and the search relaunched.