Tag: Analysis

cDNA Analysis Package 0.1.0 – Analysis of Annotated cDNAs

cDNA Analysis Package 0.1.0

:: DESCRIPTION

cDNA Analysis Package is a software suite for sequence-based bioinformatics analysis of annotated cDNAs, including tools for the detection of translation initiation and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative structure modeling of the product protein structure, identification of alternative splice forms, and comparative systems biology by metabolic pathway reconstruction. Therefore, the analyses implemented in the software system covers the levels of nucleotide sequence, codons, mRNA variants, amino acid sequence, protein structure, and metabolic pathway. Although the target unit is the cDNA, the system can be used for a variety of other data sets including EST, GSS, and complete genome data.

::DEVELOPER

Kazuharu Arakawa

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 cDNA Analysis Package

:: MORE INFORMATION

METATOOL 5.1 – Biochemical Reaction Networks Elementary Modes Analysis

METATOOL 5.1

:: DESCRIPTION

METATOOL is a Program for computing the nullspace matrix, elementary modes and other structural properties of biochemical reaction networks.This version of Metatool consists partly of script files which are compatible with octave and Matlab and partly of shared libraries that are specific for the operating system and math program. In principle the script files provide all necessary functionality, but usage of the shared libraries makes elementary mode calculation far more efficient. The purpose of this distribution is to make the operations performed by Metatool more easily understandable and to allow the users to quickly adapt and extend the scripts according to their needs.

::DEVELOPER

Department of Bioinformatics, Biocenter, University of Würzburg, Germany

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 METATOOL

:: MORE INFORMATION

Citation:

A. von Kamp and S. Schuster:
Metatool 5.0: fast and flexible elementary modes analysis.
Bioinformatics 22 (15), 2006, 1930-1931

NUPACK – Analysis and Design of Nucleic Acid Systems

NUPACK

:: DESCRIPTION

NUPACK is a growing software suite for the analysis and design of nucleic acid systems.NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.

::DEVELOPER

NUPACK Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NUPACK

:: MORE INFORMATION

Citation:

.N. Zadeh, C.D. Steenberg, J.S. Bois, B.R. Wolfe, M.B. Pierce, A.R. Khan, R.M. Dirks, N.A. Pierce.
NUPACK: analysis and design of nucleic acid systems.
J Comput Chem, 32, 170–173, 2011.

BiLayout 1.0 – Cytoscape plugin for Analysis & Visualization of Molecular Interaction Networks

BiLayout 1.0

:: DESCRIPTION

BiLayout is a Java plugin for Cytoscape, a software platform for the analysis and visualization of molecular interaction networks. This plugin computes a bipartite network layout for 2 user-selected groups of nodes.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BiLayout

:: MORE INFORMATION

STRuster 3.1 – Comparison and Analysis of Alternative Structural Models

STRuster 3.1

:: DESCRIPTION

STRuster is a method for clustering alternative structural models corresponding to different structure determination experiments. Alternative structural models, determined by X-ray crystallography or NMR spectroscopy, are frequently available for a given protein. These models can present significant structural dissimilarity.  The structures are classified according to backbone structure similarity.

::DEVELOPER

Francisco S. Domingues , Max-Planck-Institut Informatik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

STRuster

:: MORE INFORMATION

Citation:

Domingues, F. S.; Rahnenfuhrer, J.; Lengauer, T.,
Conformational analysis of alternative protein structures.
Bioinformatics 2007, 23 (23), 3131-8.

Recco 0.93 – Recombination Analysis Using Cost Optimization

Recco 0.93

:: DESCRIPTION

Recco (Recombination Analysis Using Cost Optimization) analyzes alignments of sequences that evolved subject to recombination and mutation. The analysis provides evidence as to whether a dataset contains recombination, which sequence is a recombinant and where the recombination breakpoints are. The analysis is based on explaining one sequence with all other sequences in the alignment using mutation and recombination. A parametric analysis of the parameter alpha, which weights recombination cost against mutation cost, yields additional information as to which sequence might be recombinant.

::DEVELOPER

Jochen Maydt

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 Recco

:: MORE INFORMATION

Citation:

Maydt, J. and T. Lengauer (2006).
“Recco: Recombination Analysis Using Cost Optimization.”,
Bioinformatics 2006, 22(9):1064-1071, doi:10.1093/bioinformatics/btl057.

DensityFit 1.0 – Analysis of Electronic Density Map for Protein

DensityFit 1.0

:: DESCRIPTION

DensityFit combines a low-resolution electronic density map for a protein (usually obtained by electron microscopy) and an atomic-resolution structure (usually obtained by X-ray crystallography) of the same protein in a different conformation in order to predict the atomic-resolution structure of the conformation described by the density map.

::DEVELOPER

Konrad Hinsen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DensityFit

:: MORE INFORMATION

Citation:

K Hinsen, N Reuter, J Navaza, D L Stokes, and J J Lacapere
Normal mode based fitting of atomic structure into electron density maps:application to SR Ca-ATPase
Biophys. J. 88:818-827 (2005)

TinyQuant v1.55 – Gel Image Analysis

TinyQuant v1.55

:: DESCRIPTION

TinyQuant is a miniature utility for gel image analysis. Useful for integrating densities of gel bands in 16 bit greyscale (PC or Mac format “.gel” or TIFF files) or 24 bit RGB TIFF images, and for converting these to 8 bit greyscale TIFFs. Also useful for generating optimised 8 bit greyscale images from 24 bit RGB scans.

::DEVELOPER

Iscove Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

TinyQuant

:: MORE INFORMATION

Gel Analyzer 2010a – 1D Gel Electrophoresis Image Analysis

Gel Analyzer 2010a

:: DESCRIPTION

GelAnalyzer is a free 1D gel electrophoresis image analysis software .The process of gel image analysis is straightforward and covers all the main aspects of evaluation from automatic lane detection to precise molecular weight calculations. Many tools help you to improve the accuracy of gel evaluation, such as background subtraction methods and Rf calibration. These features make GelAnalyzer a real solution to gel image analysis in cost sensitive enviroments. With GelAnalyzer you don’t need expensive gel documentation system for simple image evaluation. You may obtain the gel image with a common digital camera, or even with your cell phone, and use GelAnalyzer to get the results in just a few seconds.

::DEVELOPER

lazarsoftware.com

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

Gel Analyzer

:: MORE INFORMATION

By downloading, copying or installing any version of GelAnalyzer you accept to be bound by the End User Licence Agreement.

CP ATLAS 2.0 – Thin Layer and Gel Analysis Software

CP ATLAS 2.0

:: DESCRIPTION

CP ATLAS is a software to analyze TLC and gel images. With CP ATLAS you don’t need a professional densitometer for simple quantitative analysis. You can use a simple digital camera, office scanner or mobile phone to get a picture. With CP ATLAS the analysis takes only a few seconds, and you can copy the results to your spreadsheet software for further usage.

::DEVELOPER

lazarsoftware.com

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

CP ATLAS

:: MORE INFORMATION