BLAST

Overview

The BLAST (Basic Local Alignment Search Tool) tool compares input sequences with datasource to identify homologous sequence matches.

Basic Usage

Paste your sequence (with or without a FASTA header) into the query input text box. Transcript sequence can be extracted by type in a gene ID into the Load example text box or upload a sequence file (Less than 100 MB)with the upload file function. Then click and select the desired dataset from the lists of available BLAST databases and click the BLAST! Button at the bottom of the page.

BLAST plugin uses standard default NCBI BLAST options. However users can change the following advanced options:

Option	Description
Scoring matrix	Substitution matrix that determines the cost of each possible residue mismatch between query and target sequence. See BLAST substitution matrices for more information.
Filtering	Whether to remove low complexity regions from the query sequence.
E-value cutoff	The maximum expectation value of retained alignments.
Query genetic code	Genetic code to be used in blastx translation of the query.
DB genetic code	Genetic code to be used in blastx translation of the datasets.
Frame shift penalty	Out-of-frame gapping (blastx, tblastn only) [Integer] default = 0.
Number of results	The maximum number of results to return.

BLAST results

BLAST Results page will be automatically reloaded until the search results are successfully retrieved. BLAST results are organized into a table containing Query ID, Hit ID, Average bit score (top), Average e-value (lowest), Average identity (av. similarity) and Links. Clickable BLAST results display the corresponding region of identified homology within the JBrowse tool, where the matching region is shown.

Implementation

BLAST search tool is implemented using NCBI Blast (v2.2.26) and a backend PostgresSQL Chado database. We use PHP, JavaScript, XSL, Perl and d3js, Drupal libraries to improve Open Source GMOD Bioinformatic Software Bench server to provide a graphical user interface.