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News

Aug 2013
yoshiko version 2.0

We have released yoshiko version 2.0, a mature version of our cluster editing algorithm. It has been implemented mostly by Emanuel Laude and contains a lot of helpful redcution rules from fixed parameter algorithmics and a powerful heuristic for large data sets.

24 Aug 2011
natalie version 2.0

We have released natalie version 2.0, a mature version of our network alignment algorithm.

27 Jun 2011
side chain placement

scp is a package that contains our code for exact side chain placement as used in a recent paper in Optimization Letters.

5 Mar 2010
heinz and BioNet

heinz now works together with the BioNet package.

17 Dec 2008
yoshiko/charles

The yoshiko/charles code is now online. The tool solves the cluster editing problem as well as its directed "cousin", the transitivity editing problem, to provable optimality.

1 Sep 2008
planet lisa moves to Amsterdam

The planet lisa project is now based at the Centre for Mathematics and Computer Science (CWI) in Amsterdam, The Netherlands.

20 Jul 2008
ISMB 2008

Our paper Identifying Functional Modules in Protein-Protein Interaction Data: An Integrated Exact Approach has won the oustanding paper award at ISMB 2008 in Toronto, Canada. See the heinz section for more information on our software to discover optimal subnetworks with respect to our signal-based scoring scheme of p-values.

Jul 2008
ISMB 2008

We will give a presentation at ISMB 2008 on Identifying Functional Modules in Protein-Protein Interaction Data: An Integrated Exact Approach. Our software is available as the heinz package.

Oct 07
Algorithmic Operations Research

Our theoretical lara paper has been accepted for publication in Algorithmic Operations Research.

27 Jul 07
BMC Bioinformatics

The paper describing the lara program has been accepted for publication in BMC Bioinformatics.

28 Jun 07
4SALE support for lara

lara has been integrated into the RNA alignment and editing framework 4SALE. Get the latest lara version that is compatible with 4SALE.

Download

Download selected LiSA tools or the whole library.

lara

lara is the oldest member of the LiSA family. Given a number of RNA sequences in standard formats, it will produce a high-quality structural alignment based on the Lagrangian relaxation technique. More information can be found at the lara page.

Note that lara has also been integrated in the 4Sale tool, which is developed by the University of Würzburg (obacht link).

If you find lara useful for your own research, please cite the following paper:

Markus Bauer, Gunnar W. Klau, and Knut Reinert
Accurate Multiple Sequence-Structure Alignment of RNA Sequences Using Combinatorial Optimization.
Technical Report, Department of Mathematics ands Computer Science, Free University Berlin. TR-B-07-06, March 2007.


Further technical details can be found in

Markus Bauer, Gunnar W. Klau, and Knut Reinert
An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment.
Technical Report, Department of Mathematics ands Computer Science, Free University Berlin. TR-B-07-07, March 2007.

Markus Bauer, Gunnar W. Klau, and Knut Reinert
Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Relaxation.
In Proceedings of the 1st International Symposium on Computational Life Science (CompLife-05), pages 217-228, 2005.

Markus Bauer and Gunnar W. Klau
Structural Alignment of Two RNA Sequences with Lagrangian Relaxation.
In Proceedings of the 15th Annual International Symposium on Algorithms and Computation (ISAAC-04), pages 113-123, 2004.

version date link description comments
1.1 obacht lara 1.1 version used for computations in link to papers current stable version
0.9 obacht lara 0.9 old version used for computations in link to paper and link to paper not supported anymore

paul

paul is based on a reimplentation of the original Lancia/Caprara approach for computing the maximal contact map overlap of two protein structures. We have extended the method to do multiple protein alignments.

version date link
0.9 soon paul 0.9

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Topic revision: r5 - 04 Jun 2007, GunnarKlau
 
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