The fastacmd tool was developed by Aureliano Bombarely to interface with NCBI's wwwblast directly. However, in my project, I was tasked to implement this tool separately from BLAST. Since I am maintaining an intranet site on an Apache server, I have decided to use PHP to interface with the wwwfastacmd script (fastacmd.cgi) directly.
The script relies on using the exec() function in PHP to run the fastacmd command and return the output. Therefore, safe_mode has to be disabled in your directory. See installation instructions for more information.
The code has been updated to be HTML5 compliant.
As HTML5 is used as the markup language, you will need to enable support for HTML5 in older browsers, although this has not been a major issue in my implementation, as most of my users are using browsers that support the new <!doctype html> declaration. If majority of your users are using antiquated versions of IE, encourage them to upgrade — if that is not possible, implement HTML5shiv to allow IE to recognize HTML5 elements.
This project relies on PHP, so ensure that you have it installed on your server. If you are unsure if PHP is installed in your server, create a file with a line <?php phpinfo(); ?> and try to load the page in your browser. If a page displaying all the details of your PHP installation appears, it means that PHP has been installed correctly and is running on your server. I recommend using the latest version of PHP. This script has been tested to be working on v5.2 onwards, although most of the extensive testing has been carried out on v5.3.5.
The files can be open, edited and saved with any text editing software out there, although I personally use Sublime Text because of it's extensive support for syntax highlighting in various languages.
I have been relying on the (legacy) BLAST executables of v2.2.26, although NCBI hosts a publicly-accessible FTP directory containing various versions of it. As this project uses a deprecated command, fastacmd to comb the database, I would not expect this script to work with binaries from v2.2.30 and onwards.. I promise to look into using blastdbcmd instead in the near future.
The following files are necessary for fastacmd to work:
- fastacmd.php
- fastacmd.cgi
- fastacmd-exec.php
- fastacmd-form.php
You should note that there are no stylesheet provided. You can style the output in any way you want, although I strongly recommend using a CSS reset.
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Download the files. You can place the files anywhere on your server.
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You will have to know where the BLAST executables are installed in your system. You will need the path to the blast executables, /path/to/blast/binaries (for example:
/usr/bin/ncbi-blast-2.2.26/bin), so that you can set the environment in the CGI script. Remember to download the correct BLAST binaries/executables for the appropriate OS. -
Update the
$db_rootvariable in fastacmd.cgi so that it points to the directory where your BLAST databases can be found. -
Add the list of databases that you want to include in your fastacmd in fastacmd-form.php, for example:
<select id="seqret-db" name="db"> <option value="[database_name.fa]">Database description</option> </select>
The database name should only contain the filename of the database file (typically in
.fa- FASTA format). The absolute path to the databases are already handled in step 3. -
Update the absolute path to fastacmd.cgi in fastacmd-exec.php. The absolute path is required by PHP
exec()function to run the CGI file. -
You will also need to disable the safe_mode in PHP, or else the PHP
exec()function will not work. Please contact your system/server administrator for more details. -
You might want to allow
.cgifiles that not located within the rootcgi-binfolder to be executed.AddHandler cgi-script .cgi Options +ExecCGI -
Also, you might want to
chmodthe executable CGI files to755and beyond to allow the files to be executed.
See this projet in action at Lotus Base, a genomic resource for the model organism Lotus japonicus.