Difference between revisions of "PASA"

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{{#if: {{#var: mod}}|==Execution Environment and Modules==
==Required Modules==
[[Modules|modules documentation]]
* HPC_PASA_BIN - executable directory.
* HPC_PASA_BIN - executable directory.
* HPC_PASA_CONF - config file directory.
* HPC_PASA_CONF - config file directory.

Revision as of 16:55, 10 August 2012


pasa website  

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

modules documentation


  • pasa
  • HPC_PASA_BIN - executable directory.
  • HPC_PASA_CONF - config file directory.

How To Run

Tools and variables

  • UNIVECDB environment 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.

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.