guoyu07 / tripal_blast

DEVELOPMENT Repo for Tripal Blast. For official releases & documentation go to drupal.org

INTRODUCTION

This module provides a basic interface to allow your users to utilize your server's NCBI BLAST+.

Specifically it provides two forms, one for nucleotide queries and another for protein queries. Currently only blastn and blastp are supported but in the future you will be able to select either a nucleotide or a protein database to BLAST against regardless of the type of query and this module will decide which BLAST program to use based on the combination of query/database type (ie: if you selected a protein database on the nucleotide BLAST form then blastx would be used).

BLAST submissions result in the creation of Tripal jobs which then need to run from the command-line. This ensures that long running BLASTS will not cause page time-outs but does add some management overhead and might result in longer waits for users depending on how often you have cron set to run Tripal jobs. A Tripal Jobs Daemon is under development to allow these jobs to be run almost as soon as they are submitted.

The BLAST results page is an expandable summary table with each hit being listed as a row in the table with query/hit/e-value information. The row can then be expanded to include additional information including the alignment. Download formats are under development to allow users to download these results in the familiar tabular or HTML NCBI formats.

Highlighted Functionality

• Supports blastn and blastp with separate forms depending upon the query type.
• Simple interface allowing users to paste or upload a query sequence and then select from available databases. Additionally, a FASTA file can be uploaded for use as a database to BLAST against.
• Tabular Results listing with alignment information available.
• Completely integrated with Tripal Jobs providing administrators with a way to track BLAST jobs and ensuring long running BLASTs will not cause page time-outs
• BLAST databases are made available to the module by creating Drupal Pages describing them. This allows administrators to use the Drupal Field API to add any information they want to these pages.

Installation

1. Install NCBI BLAST+ on your server (Tested with 2.2.26+). There is a package available for Ubuntu to ease installation.
2. Install this module as you would any Drupal module (ie: download, unpack in sites/all/modules and enable through http://[your site]/admin/modules)
3. Create "Blast Database" nodes for each dataset you want to make available for your users to BLAST against. BLAST databases should first be created using the command-line makeblastdb program with the -parse_seqids flag.

Customization

The BLAST module forms can be styled using CSS stylesheets in your own theme. By default it will use the default form themeing provided by your particular Drupal site allowing it to feel consistent with the look-and-feel of your Tripal site without customization being needed.

Additionally, the results page, waiting pages and the alignment section of the results page have their own template files (blast_report.tpl.php, blast_report_pending.tpl.php, and blast_report_alignment_row.tpl.php, respectively) which can easily be overridden in your own theme providing complete control over the look of the BLAST results.