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README.md

@@ -32,7 +32,8 @@ Highlighted Functionality
  - 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.
+ - 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
@@ -40,6 +41,8 @@ Highlighted Functionality
    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
@@ -55,6 +58,11 @@ Installation
    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](https://github.com/tripal/tripal/tree/7.x-3.x/tripal_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](https://github.com/LegumeFederation/cvitjs) and extract
@@ -79,3 +87,22 @@ 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
+------------------------------
+<table>
+<tr><th></th><th><a href="project/tripal_blast">Tripal BLAST UI</a></th><th><a href="project/tripal_blast_analysis">Tripal BLAST Analysis</a></th></tr>
+<tr><th>Provides an interface to execute BLASTs</th><td>Yes</td><td>No</td></tr>
+<tr><th>Display BLAST Results to users</th><td>After BLAST submission</td><td>On associated feature pages</td></tr>
+<tr><th>Load BLAST Results into Chado</th><td>No</td><td>Yes</td></tr>
+</table>
+**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</li>
+ - Better results output including a summary table and eventually an image</li>
+ - Ability to Email user when BLAST is done</li>
+ - Automatic cleaning up of BLAST job files after 1 week (make time frame configurable)</li>