PASA
Revision as of 17:24, 24 September 2013 by Moskalenko (talk | contribs)
Description
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.
Required Modules
Serial
- pasa
System Variables
- HPC_{{#uppercase:pasa}}_DIR - installation directory
- HPC_PASA_BIN - executable directory.
- HPC_PASA_CONF - config file directory.
Additional Information
Tools and variables
UNIVECDBenvironment variable is set to the location of the UniVec database for use by seqclean.
Databases
- 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:
MYSQLDB=test_run_pasa
The example configuration files are located in /apps/pasa/20110520/pasa_conf ($HPC_PASA_CONF) directory.
Web Portal
You can visualize the results of your PASA run by going to the "http://pasa2.hpc.ufl.edu/cgi-bin/status_report.cgi?db=$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. Pasa 1.5 URIs can be reached at http://pasa.hpc.ufl.edu.