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+################################################################################
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+INTRODUCTION
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+------------
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+This module provides a basic interface to allow your users to utilize your
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+server's NCBI BLAST+.
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+
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+Specifically it provides two forms, one for nucleotide queries and another for
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+protein queries. Currently only blastn and blastp are supported but in the future
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+you will be able to select either a nucleotide or a protein database to BLAST
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+against regardless of the type of query and this module will decide which BLAST
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+program to use based on the combination of query/database type (ie: if you
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+selected a protein database on the nucleotide BLAST form then blastx would
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+be used).
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+
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+BLAST submissions result in the creation of Tripal jobs which then need to run
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+from the command-line. This ensures that long running BLASTS will not cause
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+page time-outs but does add some management overhead and might result in longer
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+waits for users depending on how often you have cron set to run Tripal jobs.
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+A Tripal Jobs Daemon is under development to allow these jobs to be run almost
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+as soon as they are submitted.
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+
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+The BLAST results page is an expandable summary table with each hit being
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+listed as a row in the table with query/hit/e-value information. The row can
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+then be expanded to include additional information including the alignment.
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+Download formats are under development to allow users to download these
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+results in the familiar tabular or HTML NCBI formats.
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+
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+Highlighted Functionality
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+-------------------------
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+ - Supports blastn and blastp with separate forms depending upon the query
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+ type.
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+ - Simple interface allowing users to paste or upload a query sequence and
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+ then select from available databases. Additionally, a FASTA file can be
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+ uploaded for use as a database to BLAST against.
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+ - Tabular Results listing with alignment information available.
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+ - Completely integrated with Tripal Jobs providing administrators with a
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+ way to track BLAST jobs and ensuring long running BLASTs will not cause
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+ page time-outs
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+ - BLAST databases are made available to the module by creating Drupal Pages
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+ describing them. This allows administrators to use the Drupal Field API to
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+ add any information they want to these pages.
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+
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+Installation
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+------------
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+1. Install NCBI BLAST+ on your server (Tested with 2.2.26+). There is a
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+ package available for Ubuntu to ease installation.
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+2. Install this module as you would any Drupal module (ie: download, unpack
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+ in sites/all/modules and enable through http://[your site]/admin/modules)
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+3. Create "Blast Database" nodes for each dataset you want to make available
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+ for your users to BLAST against. BLAST databases should first be created
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+ using the command-line makeblastdb program with the -parse_seqids flag.
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+
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+Customization
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+-------------
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+The BLAST module forms can be styled using CSS stylesheets in your own theme.
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+By default it will use the default form themeing provided by your particular
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+Drupal site allowing it to feel consistent with the look-and-feel of your
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+Tripal site without customization being needed.
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+
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+Additionally, the results page, waiting pages and the alignment section of
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+the results page have their own template files (blast_report.tpl.php,
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+blast_report_pending.tpl.php, and blast_report_alignment_row.tpl.php,
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+respectively) which can easily be overridden in your own theme providing
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+complete control over the look of the BLAST results.
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Lacey Sanderson