The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites.
Execution Environment and Modules
To use pasa with the environment modules system at HPC the following commands are available:
Get module information for pasa:
$module spider pasa
Load the default application module:
$module load pasa
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_PASA_DIR - directory where pasa is located.
- HPC_PASA_BIN - executable directory.
- HPC_PASA_CONF - config file directory.
How To Run
Tools and variables
UNIVECDBenvironment variable is set to the location of the UniVec database for use by seqclean.
- The MySQL server used by PASA has been configured to allow the pasaadmin user to create databases with names that end in _pasa only. So, to run pasa your configuration file such as alignAssembly.config or conf.txt must have MySQL configuration similar to the following entry:
The example configuration files are located in
/apps/pasa/20110520/pasa_conf ($HPC_PASA_CONF) directory.
You can visualize the results of your PASA run by going to the "http://pasa.hpc.ufl.edu/cgi-bin/status_report.cgi?db=$MYSQL_DB" URL where "$MYSQL_DB" must be changed to the database name used for the run. Use your HPC credentials to access the protected web portal.