tripal_blast/README.md

INTRODUCTION

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

Specifically it provides blast program-specific forms (blastn, blastp, tblastn, blastx are supported). In the future, there will be a single form where you will be able to select either a nucleotide or a protein database to BLAST against regardless of the type of query and it 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. You can alternatively use the Tripal Jobs Daemon to automate running of Tripal Jobs reducing user wait time and your own workload.

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 allow users to download these results in the familiar tabular, GFF3 or HTML NCBI formats.

Highlighted Functionality

• Supports blastn, blastp, tblastn, and blastx 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 and multiple download formats (HTML, TSV, GFF3, XML) 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 and to control which databases are available to a given user based on native Drupal permissions.
• BLAST database records can be linked to an external source with more information (ie: NCBI) per BLAST database.
• Per Query result diagrams visualizing the HSPs to help users better evaluate hit quality.
• Optional Whole Genome diagrams visualizing the distribution of hits which are configurable per Blast Database.

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.
   

It's recommended that you also install the Tripal Job Daemon to manage BLAST jobs and ensure they are run soon after being submitted by the user. Without this additional module, administrators will have to execute the tripal jobs either manually or through use of cron jobs.

Set-up of Whole Genome Diagrams with CViTjs

1. Download CViTjs v0.1.0-beta and extract it at sites/all/libraries
2. Configure it via the Tripal Blast administration settings at http://[your site]admin/tripal/extension/tripal_blast/settings
3. Enable it for specific Blast Databases by editing the corresponding Tripal "Blast Database" Drupal node.
   

For more in depth help, reference the Help tab at http://[your site]/admin/tripal/extension/tripal_blast/help

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.

Comparison with other Modules

	Tripal BLAST UI	Tripal BLAST Analysis
Provides an interface to execute BLASTs	Yes	No
Display BLAST Results to users	After BLAST submission	On associated feature pages
Load BLAST Results into Chado	No	Yes

NOTE: These modules will be combined into a single download available here in the not so distant future. You will still have the flexibility to enable either one or the other or both.

Future Development

• The ability to blast against 2+ datasets at the same time

Better results output including a summary table and eventually an image

Ability to Email user when BLAST is done

Automatic cleaning up of BLAST job files after 1 week (make time frame configurable)