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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.

How To Run

Tools and variables

  • UNIVECDB environment variable is set to the location of the UniVec database for use by seqclean.