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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

modules documentation


  • 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

  • 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.

Make sure to name your pasa database as 'pasa_${USER}_$NAME' where '$NAME' is the name you want to give the database and '$USER' is your username. For example a database can be named as 'pasa_jdoe_experiment_1'.

Web Portal

You can visualize the results of your PASA run by going to "$MYSQL_DB" URI where "$MYSQL_DB" must be changed to the database name used for the run. Use your HPC credentials to access the protected web portal.

Note: Pasa2 web interface no longer has an administrative page. Go directly to status_report.cgi.

Pasa 1.5 URIs can be reached at