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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.

LiSA helpers

The planet LiSA library is now hosted in "Amsterdam"

LiSA helpers are small and useful tools created with the LiSA library. If you use one of these tools for your work please cite

G. W. Klau, M. Bauer, P. May, L. Petzold. LiSA. Library of Structural Alignment Algorithms. Manuscript, 2007. http://www.planet-lisa.net

pdb2cm

This tool reads in pdb files and outputs a contact map.

Usage

Type

$./pdb2cm -h

to get the help and the usage. The rest is quite self-explanatory.

Contact Map file-format

line contentSorted ascending
2 number of contacts (say m contacts)
1 sequence length
3..m+2 the contacts, one per line, line format: 'a b w c\n', where 'a' denotes the first position and 'b' the second position of the contact with a<b, 'w' is the corresponding contact weight (default: 1) and 'c' the contact class (default: 1)

Download

version date link
1.0 12 Jun 2007 pdb2cm 1.0

sscompare

Given two alignments and the structures for each sequence in the alignment, the program compares the structures on the base pair level. It outputs the sensitivity, specificity, and the geometric mean of the two values.

Usage

Type

$./sscompare

to get the the usage message. The rest is quite self-explanatory.

Download

version date link
1.0 20 Jun 2007 sscompare 0.1
Topic revision: r5 - 28 Apr 2015, UnknownUser
 
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