Spa : A probabilistic algorithm for spliced alignment
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.
Erik van Nimwegen and Mihaela Zavolan give permission to you and your institution
to use the Spa software for internal, research purposes, on the
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. 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. 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. Any risk associated with using the Spa software suite at your institution is with
you and your institution.
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
Spa : A Probabilistic Algorithm
for Spliced Alignment
PLoS Genetics, to appear, 2006
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: email@example.com
* - are required fields.
(Gcc version : 3.2.1;Library versions: libc.so.1,
libstdc++.so.5.0.1) containing source, documentation, and
utilities. It should run on most Linux systems.
Please report bugs and problems to us (firstname.lastname@example.org). 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
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.