PASA
Revision as of 16:55, 10 August 2012 by Moskalenko (talk | contribs) (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}")
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.
Available Versions
- 20110520
Required Modules
Serial
- pasa
- 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.
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 ($HPC_PASA_CONF) directory.
Web Portal
You can visualize the results of your PASA run by going to the "http://pasa.hpc.ufl.edu/cgi-bin/status_report.cgi?db=$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.