Mondrian Piet: Red Tree Erik van Nimwegen Group
Bioinformatics and Systems Biology

Spa : A probabilistic algorithm for spliced alignment

  1. Overview

    Spa is a computer program for aligning cDNA sequences to a genome. It uses a probabilistic Bayesian model to find the optimal alignment. To keep running times feasible we use the BLAT gfServer to identify genomic loci and return the best mapping from these loci.

    BLAT source and executables are freely available for academic, nonprofit and personal use. The source can be downloaded from and the executables from

    Spa uses a set parameters o`qrganism-dependent. Thus, some utilities are provided with the spa code for parameter estimation and post-processing.

  2. License agreement

    Erik van Nimwegen and Mihaela Zavolan give permission to you and your institution to use the Spa software for internal, research purposes, on the following conditions:

    1. 1. The Spa software suite remains at your institution and is not published, distributed, or otherwise transferred or made available to people other than institution employees and students involved in research under your supervision.
    2. 2. The Spa software suite will be used by you and/or your institution solely for non-commercial purposes, except with express permission from the authors.
    3. 3. You may provide the authors with feedback on the use of the Spa software suite in your research, and the authors are permitted to use any information you provide in making changes to the software.
    4. 4. Any risk associated with using the Spa software suite at your institution is with you and your institution.
    5. 5. The Spa software suite should be cited in any publication(s) reporting on data obtained by using it, as:

      Erik van Nimwegen, Nicodeme Paul, Robert Sheridan, and Mihaela Zavolan
      Spa : A Probabilistic Algorithm for Spliced Alignment
      PLoS Genetics, to appear, 2006

  3. Download

    If these conditions are acceptable to you Please supply your name, institution, and email address when you download the code. If you have any questions concerning this agreement, you may contact us at:


    * - are required fields.

    tar-archive (Gcc version : 3.2.1;Library versions:, containing source, documentation, and utilities. It should run on most Linux systems.

  4. Feedback

    Please report bugs and problems to us ( We welcome all feedback on the program. If there is a feature you particularly would like to see, please let us know. If you successfully compiled the program on another platform please let us know and we will distribute the executable here acknowledging you.

  5. Acknowledgments

    The Spa software suite was developed by Erik van Nimwegen and Mihaela Zavolan (Biozentrum, University of Basel, Switzerland) and was programmed by Robert Sheridan and Nicodeme Paul.