PASA

Description

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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. Template:App Location

Available Versions

• 20110520

Running the application using 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

• UNIVECDB environment 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.