Tripal BLAST Module Description

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

Setup | Functionality | Large jobs | Genome visualization

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Setup Instructions

Install NCBI BLAST+ on your server (Tested with 2.2.26+). There is a package available for Ubuntu to ease installation. Optionally you can set the path to your BLAST executable in the settings.
Optionally, create Tripal External Database References to allow you to link the records in your BLAST database to further information. To do this simply go to Tripal> Chado Modules > Databases > Add DB and make sure to fill in the Database prefix which will be concatenated with the record IDs in your BLAST database to determine the link-out to additional information. Note that a regular expression can be used when creating the BLAST database to indicate what the ID is.
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.

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Highlighted Functionality

Supports blastn, blastx, blastp and tblastx with separate forms depending upon the database/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 (this functionality can be disabled).
Tabular Results listing with alignment information and multiple download formats (HTML, TSV, 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.
BLAST database records can be linked to an external source with more information (ie: NCBI) per BLAST database.

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Protection Against Large Jobs

Depending on the size and nature of your target databases, you may wish to constrain use of this module.

Limit the number of results displayed via admin page. The recommended number is 500.
Limit the maximum upload file size in php settings. This is less useful because some very large queries may be manageable, and others not.
Repeat-mask your targets, or provide repeat-masked versions. Note that some researchers may be looking for repeats, so this may limit the usefulness of the BLAST service.

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Whole Genome Visualization

This module can be configured to use CViTjs to display BLAST hits on a genome image.

CViTjs Setup

Download CViTjs and copy the code to your webserver. It might make the most sense to put the code directly into this module's directory, in a subdirectory named js/. To download, execute the git command inside the js/ subdirectory:
git clone https://github.com/LegumeFederation/cvitjs.git
CViTjs will have a config file in its root directory named cvit.conf. This file provides information for whole genome visualization for each genome BLAST target. Make sure the config file can be edited by your web server.
(This step will be removed when the CViTjs code is repaired -03/06/18) There is a hard-coded path in the CViTjs file js/lib/require/blast_ui-config.js. Set this line to the correct path for your server:
```
baseUrl: '../../sites/all/modules/blast_ui/js/cvitjs/js/lib',
```
Enable CViTjs from the BLAST module administration page and provide the path to the root directory for the CViTjs code relative to this module. For example, js/cvitjs.
Edit the configuration file to define each genome target. These will look like:
```
[data.Cajanus cajan - genome]
conf = data/cajca/cajca.conf
defaultData = data/cajca/cajca.gff
```
Where:
- the section name, "data.Cajanus cajan - genome", consists of "data." followed by the name of the BLAST target node,
- the file "cajca.conf" is a cvit configuration file which describes how to draw the chromosomes and BLAST hits on the Cajanus cajan genome,
- and the file "cajca.gff" is a GFF3 file that describes the Cajanus cajan chromosomes.
At the top of the configuration file there must be a [general] section that defines the default data set. For example:
```
[general]
data_default = data.Cajanus cajan - genome
```
Edit the nodes for each genome target (nodes of type "BLAST Database") and enable whole genome visualization. Remember that the names listed in the CViTjs config file must match the BLAST node name. In the example above, the BLAST database node for the Cajanus cajan genome assembly is named "Cajanus cajan - genome"

Notes

The .conf file for each genome can be modified to suit your needs and tastes. See the sample configuration file, data/test1/test1.conf, and the CViTjs documentation.
Each blast target CViTjs configuration file must define how to visualize blast hits or you will not see them.
```
[blast]
feature = BLASTRESULT:match_part
glyph   = position
shape = rect
color   = #FF00FF
width = 5
```
You will have to put the target-specific conf and gff files (e.g. cajca.conf and cjca.gff) on your web server, in the directory, js/cvitjs/data. You may choose to group files for each genome into subdirectories, for example, js/cvitjs/data/cajca.
It is important to make sure that cvit.conf points to the correct data directory and the correct .gff and .conf files for the genome in question. For more information about how to create the .gff file, see the documentation.