FluxModeCalculator – Large-scale Flux mode Computation

FluxModeCalculator

:: DESCRIPTION

FluxModeCalculator is a MATLAB toolbox for computing the elementary flux modes, extreme pathways or minimal generating sets in stoichiometric models

::DEVELOPER

Jan Bert van Klinken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • MatLab

:: DOWNLOAD

 FluxModeCalculator

:: MORE INFORMATION

Citation

FluxModeCalculator: an efficient tool for large-scale flux mode computation.
van Klinken JB, Willems van Dijk K.
Bioinformatics. 2015 Dec 18. pii: btv742.

PHYSICO 2 – Computation of Properties of Protein Sequences

PHYSICO 2

:: DESCRIPTION

PHYSICO2 is an UNIX based Standalone Procedure for Computation of Physicochemical, Window-dependent and Substitution Based Evolutionary Properties of Protein Sequences along with Automated Block Preparation Tools.

::DEVELOPER

PHYSICO team

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PHYSICO

:: MORE INFORMATION

Citation:

PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2.
Banerjee S, Gupta PS, Nayek A, Das S, Sur VP, Seth P, Islam RN, Bandyopadhyay AK.
Bioinformation. 2015 Jul 31;11(7):366-8. doi: 10.6026/97320630011366.

POPS* 1.6.4 – Fast and Accurate Computation of Surface Areas of Proteins and Nucleic Acids

POPS* 1.6.4

:: DESCRIPTION

POPS* (Parameter optimized surfaces) is a fast algorithm to calculate solvent accessible surface areas (SASAs) of proteins and nucleic acids at atomic (default) and residue (coarse-grained) level. Atomic and residue area parameters have been optimised versus an accurate all-atom method (Naccess). Residue areas (coarse-grained) are simulated with a single sphere centered at the C-alpha atom for amino acids and at the P atom for nucleotides.

::DEVELOPER

Franca Fraternali, Luigi Cavallo, Jens Kleinjung et al

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 POPS*

:: MORE INFORMATION

Citation:

Fraternali, F. and Cavallo, L.,
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome.
Nucleic Acids Research 30 (2002) 2950-2960

CentiLib – Computation of network centralities

CentiLib

:: DESCRIPTION

CentiLib is an Add-on for the computation and investigation of weighted and unweighted centralities in biological networks. Even though CentiLib was developed to integrate the computation of centralities into as many tools for the visualisation and analysis of biological networks as possible, it can be used for other types of networks, too.

::DEVELOPER

Johannes Gräßler.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CentiLib 

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Apr 15;28(8):1178-9. Epub 2012 Mar 5.
CentiLib: comprehensive analysis and exploration of network centralities.
Gräßler J, Koschützki D, Schreiber F.

zipHMM 1.0.1 – Library for very fast Likelihood Computations for Hidden Markov Models

zipHMM 1.0.1

:: DESCRIPTION

zipHMM is a library for hidden Markov models that exploits repetitions in strings to greatly speed up the calculations of the log likelihood of a sequence.

::DEVELOPER

Thomas Mailund

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 zipHMM

:: MORE INFORMATION

Citation:

zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.
Sand A, Kristiansen M, Pedersen CN, Mailund T.
BMC Bioinformatics. 2013 Nov 22;14:339. doi: 10.1186/1471-2105-14-339.

FastPval – Fast Two Stage P-value Computation Software

FastPval

:: DESCRIPTION

FastPval is a two stage p-value computation software which compute the empirical p-value by two stage ranking strategy, it can produce very low P-value based on huge dataset. This fast and powerful tool takes advantage of a delicate cutoff which separate the exactly significant area. Compared to the traditional ranking method, Tspvc has a good time efficiency, lower memory consuming and tiny storage spaces with high accuracy.

::DEVELOPER

Bioinformatics Group, HKU Department of Biochemistry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

FastPval

:: MORE INFORMATION

Citation

Mulin Jun Li, Pak Chung Sham, and Junwen Wang
FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution.
Bioinformatics. 2010 Nov 15;26(22):2897-9. Epub 2010 Sep 21.

iTagPlot 1.0 – Computation and Interactive Visualization of Tag Density

iTagPlot 1.0

:: DESCRIPTION

iTagPlot is a tool to accurately compute and interactively visualize tag density (read coverage)from genomic sequencing data.

::DEVELOPER

iTagPlot team

:: SCREENSHOTS

iTagPlot

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • JRE

:: DOWNLOAD

 iTagPlot

:: MORE INFORMATION

Citation

iTagPlot: An accurate computation and interactive drawing tool for tag density plot.
Kim SH, Ezenwoye O, Cho HG, Robertson KD, Choi JH.
Bioinformatics. 2015 Mar 19. pii: btv166

WEBnm@ 2.0 – Web-server for Normal Mode Analysis of proteins

WEBnm@ 2.0

:: DESCRIPTION

WEBnm@ is meant to provide users with simple and automated computation and analysis of low-frequency normal modes for proteins.

::DEVELOPER

Nathalie Reuter , Uni Computing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Dec 30;15(1):6597. [Epub ahead of print]
WEBnm@ v2.0: Web server and services for comparing protein flexibility.
Tiwari SP, Fuglebakk E, Hollup SM, Skjærven L, Cragnolini T, Grindhaug SH, Tekle KM, Reuter N.

WEBnm@: a web application for normal mode analysis of proteins.
S.M.Hollup, G.Salensminde and N.Reuter.
BMC Bioinformatics (2005), 6(1): 52

DTWave 201405 – Dynamic Time Warping for Spectrogram Alignment and AVErage Sequence Computation

DTWave 201405

:: DESCRIPTION

DTWave is a tool for analysing sound sequences, it allows to
– measure a pairwise distance between two or more sounds,
– compute an average sequence from a pair of sounds.

::DEVELOPER

the New Zealand Bioinformatics Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • C Compiler

:: DOWNLOAD

 DTWave

:: MORE INFORMATION

Citation:

Louis Ranjard, Michael G. Anderson, Matt J. Rayner, Robert B. Payne, Ian McLean, James V. Briskie, Howard A. Ross, Dianne H. Brunton, Sarah M. N. Woolley, Mark E. Hauber,
Bioacoustic distances between the begging calls of brood parasites and their host species: a comparison of metrics and techniques,
Behavioral Ecology and Sociobiology, 2010

DNASIZE – Computation of size of DNA and Protein Fragments from Their Electrophoretic Mobility

DNASIZE

:: DESCRIPTION

DNASIZE allows to compute the length of DNA or protein fragments from its electropheric mobility using a graphical method.

DNASIZE Online version

::DEVELOPER

G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • DOS

:: DOWNLOAD

  DNASIZE 

:: MORE INFORMATION

Citation

Raghava, G. P. S. (2001)
A web server for computing size of DNA/Protein fragment using graphical method.
Biotech Software and Internet Report 2:198-200.