CPSP Tools 4.8.0 – Constraint-based Protein Structure Prediction

CPSP Tools 4.8.0

:: DESCRIPTION

CPSP-tools package provides programs to solve exactly and completely the problems typical of studies using 3D lattice protein models. Among the tasks addressed are the prediction of globally optimal and/or suboptimal structures as well as sequence design and neutral network exploration.

::DEVELOPER

Bioinformatics Group
Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CPSP Tools

:: MORE INFORMATION

Citation

Martin Mann, Sebastian Will, and Rolf Backofen.
CPSP-tools – Exact and Complete Algorithms for High-throughput 3D Lattice Protein Studies.
BMC Bioinformatics, 9, 230, 2008.

MONGOOSE 1.1 – Structural Analysis and Refinement of Constraint-based Metabolic Networks

MONGOOSE 1.1

:: DESCRIPTION

MONGOOSE (MetabOlic Network GrOwth Optimization Solved Exactly) is a package for structural analysis and refinement of constraint-based metabolic networks. Unlike other existing software, MONGOOSE uses exact rational arithmetic, which makes its results certifiably accurate.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 MONGOOSE

:: MORE INFORMATION

Citation:

Genome Biol. 2012 Jan 31;13(1):r6. doi: 10.1186/gb-2012-13-1-r6.
MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis.
Chindelevitch L, Stanley S, Hung D, Regev A, Berger B.

EvoFBA – Simulating Evolution of Constraint Based Models of Cellular Metabolism

EvoFBA

:: DESCRIPTION

EvoFBA is a MATLAB implementation of the evolutionary and ecological dynamics simulations of growing E.coli populations

::DEVELOPER

OSS-Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOs
  • MatLab

:: DOWNLOAD

EvoFBA

:: MORE INFORMATION

Citation

BMC Evol Biol, 16 (1), 163
Metabolic Modelling in a Dynamic Evolutionary Framework Predicts Adaptive Diversification of Bacteria in a Long-Term Evolution Experiment
Tobias Großkopf, Jessika Consuegra , Joël Gaffé, John C Willison, Richard E Lenski, Orkun S Soyer, Dominique Schneider

CS-PSeq-Gen 1.0 – Simulation of Protein Sequences under Constraints

CS-PSeq-Gen 1.0

:: DESCRIPTION

CS-PSeq-Gen is a program derived from PSeq-Gen, a program developed by Nick C. Grassly and Andrew Rambaut, designed to simulate the evolution of protein sequences along evolutionary trees. CS-PSeq-Gen modifications are related to the aim of simulating the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny: the “root sequence” that initiates the simulation, or the rate heterogeneity among sites are specific on each particular protein family. CS-Pseq-Gen will allow simulations to take such information into account. As well, exploring the evolution of one protein family and testing hypotheses makes often it necessary to have some control on the variability of the parameters. CS-PSeq-Gen will allow some control on the simulated tree / branch lengths around an average value. Finally, a particular category of applications for such simulations is the search for the significant co-evolution of sites. CS-PSeq-Gen offers some facilities to generate sequences under such hypotheses, and propose a basic scheme for their detection, that can be easily adapted by programmers.

::DEVELOPER

P. Tufféry  (tuffery@ebgm.jussieu.fr )

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CS-PSeq-Gen

:: MORE INFORMATION

Citation

Tufféry, P.
CS-PSeq-Gen: Simulating the evolution of protein sequence under constraints
Bioinformatics, Volume 18, Number 7, July 2002 , pp. 1015-1016(2)

CLASS 2.1.2 – Constraint-based Local Assembly and Selection of Splice Variants

CLASS 2.1.2

:: DESCRIPTION

CLASS is a software tool  for accurately assembling splice variants using local read coverage patterns of RNA-seq reads, contiguity constraints from read pairs and spliced reads, and optionally information about gene structure extracted from cDNA sequence databases.

::DEVELOPER

Li Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsx/Linux

:: DOWNLOAD

 CLASS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 5:S14. doi: 10.1186/1471-2105-14-S5-S14. Epub 2013 Apr 10.
CLASS: constrained transcript assembly of RNA-seq reads.
Song L, Florea L.

PSILC 1.21 – Pseudogene Inference from loss of Constraint

PSILC 1.21

:: DESCRIPTION

PSILC (pseudogene inference from loss of constraint) incorporates novel methods for separating pseudogenes from functional genes.

::DEVELOPER

Dr Lachlan J Coin and Durbin R

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PSILC

:: MORE INFORMATION

Citation

Improved techniques for the identification of pseudogenes.
Coin L and Durbin R
Bioinformatics 2004;20 Suppl 1;i94-100

FBA-SimVis 1.91 – Dynamic Visualisation of Constraint-based Metabolic Models

FBA-SimVis 1.91

:: DESCRIPTION

FBA-SimVis  (FBASimVis) is a VANTED Add-on for the constraint-based analysis of metabolic models with special focus on the dynamic and visual exploration of metabolic flux data resulting from model analysis.

::DEVELOPER

 Eva Grafahrend-B26elau and members of the groups Plant Bioinformatics and Systems Biology.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 FBA-SimVis

:: MORE INFORMATION

Citation

Eva Grafahrend-Belau1,, Christian Klukas, Björn H. Junker and Falk Schreiber
FBA-SimVis: interactive visualization of constraint-based metabolic models
Bioinformatics (2009) 25 (20): 2755-2757.

ConTest 1.0.2 – Test Constraints in Proteins

ConTest 1.0.2

:: DESCRIPTION

ConTest (Contstraint Testing) is a program to detect positions within a set of aligned protein sequences that are evolutionarily constrained.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Bio++

:: DOWNLOAD

ConTest

:: MORE INFORMATION

Anchored DIALIGN 2.2.2 – Multiple Sequence Alignment with User-defined Constraints

Anchored DIALIGN 2.2.2

:: DESCRIPTION

Anchored DIALIGN is a WWW server for multiple alignment of protein and nucleic acid sequences using DIALIGN with user-defined anchor points.Alignments can be created either fully automatically or by using a list of user-defined constraints. By specifying such anchor points, the user can force the program to align selected segments of the sequences to each other. The remaining parts of the sequences are then aligned automatically, respecting the constraints imposed by the selected anchor points.

Anchored DIALIGN Online Version

::DEVELOPER

Burkhard Morgenstern et al.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Anchored DIALIGN

:: MORE INFORMATION

Citation

B. Morgenstern, S.J. Prohaska, D. P?hler, P.F. Stadler (2006)
Multiple sequence alignment with user-defined anchor points
Algorithms for Molecular Biology 1,6.