Last updated August 12, 2009.
About the document
This document is a user manual for the Boltzmann
Likelihood software written by Mirela Andronescu.
Index
1. Introduction to BL
Boltzmann Likelihood (BL) is a computational approach to RNA free
energy parameter estimation. It maximizes the conditional likelihood of
the known structures in a set of RNA sequences with known secondary
structures used for training. This algorithm is similar to the
CONTRAfold algorithm (Do et al, 2006).
2. Copyright and disclaimer
Copyright
The BL algorithm and code is copyrighted under GNU General
Public Licence by Mirela Andronescu, Anne Condon and Holger
Hoos, Department of Computer Science, University of British Columbia.
Disclaimer
Although the authors have made every effort to ensure that BL
correctly implements the underlying models and fullfills the functions
described in the documentation, neither the authors nor the University
of British Columbia guarantee its correctness, fitness for a particular
purpose, or future availability.
3. Using BL
BL uses the IPOPT
non-linear optimizer. In order to run BL with IPOPT, you have to have
the following packages:
- MultiRNAFold, follow the steps here.
MultiRNAFold contains functions for the computation of the partition
function, base pair probabilities and partition function gradient.
- IPOPT, follow the steps here.
- Matlab.
- BL_ipopt, that you can download from here.
To run BL, type:
bin/BLlearn_ipopt.pl config/config_example.txt
This will create a directory with a complicated name in results.
4. Troubleshooting
Please let know andrones at cs dot ubc dot ca if you have
problems running BL.
5. History
- August 12, 2009, version 2.0 was released. Major
changes have been applied since version 1.0.
- Added many options, configuration files, optimized the
code etc etc etc.
- Added the IPOPT variant
- 2007, version 0.1 of this software, under the name
"Maximum Likelihood", was used by Andronescu et al, 2007.
6.
References
- BL v1.0 was used in (the name in the paper was Maximum
Likelihood):
- M. Andronescu, A. Condon, H.H. Hoos, D.H. Mathews and
K.P. Murphy,
"Efficient parameter estimation for RNA secondary structure
prediction", Bioinformatics (2007) 9(1):340,
ISMB/ECCB 2007.
- BL v2.0 was used in:
- M. Andronescu, Computational approaches for RNA energy
parameter
estimation, PhD. Thesis, Dept. of Computer Science, University of
British Columbia (2008).
Please
cite one of the above if you use BL in your work.