MeV 4.9.0 – Multiple Experiment Viewer

MeV 4.9.0

:: DESCRIPTION

MeV is a desktop application for the analysis, visualization and data-mining of large-scale genomic data. It is a versatile microarray tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery.

MeV allows the user to view processed microarray slide representations and identifies genes and expression patterns of interest. Slides can be viewed one at a time in detail or in groups for comparison purposes. A variety of normalization algorithms and clustering analyses allow the user flexibility in creating meaningful views of the expression data.

MeV generates informative and interrelated displays of expression and annotation data from single or multiple experiments. A huge array of alrogithms are included in MeV modules, and are available at a button-click, such as K-means clustering, Hierarchical clustering, t-Tests, Significance Analysis of Microarrays, Gene Set Enrichment Analysis, and EASE.

::DEVELOPER

J. Craig Venter Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OS X /Linux
  • Java

:: DOWNLOAD

MeV ; manual.

:: MORE INFORMATION

Referencing MeV

Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques. 2003 Feb;34(2):374-8.

J3DPSV 1.0 – Java Three-dimensional (3D) Protein Structure Viewer

J3DPSV 1.0

:: DESCRIPTION

J3dPSV is a graphical application package for viewing and modeling of three dimensional structures of protein structure, including multiple chain sequence table and a three-dimensional (3D) protein structure viewer.

:: DEVELOPER

Hyun Seok Park

:: SCREENSHOTS

J3DPSV

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • JAVA

:: DOWNLOAD

 J3DPSV

:: MORE INFORMATION

Citation

Chun, Yoo Jin, Il Ham, Seong, Yang, San Duk, Rhie, Arang, Park, Hyun Seok
Refactoring the code for visualizing protein database information in a 3D viewer for software reusability
Genomics & Informatics, 6:50-53, MAR 31 2008

FinchTV 1.5 – Trace Viewer

FinchTV 1.5

:: DESCRIPTION

FinchTV is the popular way to view DNA sequence traces. FinchTV started as the only chromatogram viewer that can display an entire trace in a scalable multi-pane view. And it leads the way with raw data views, BLAST searching and the ability to reverse complement sequences and traces.

::DEVELOPER

Geospiza, Inc.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux

:: DOWNLOAD

FinchTV

:: MORE INFORMATION

Reveal – Viewer for Automated active-site Predictions for Polypeptides

Reveal

:: DESCRIPTION

Reveal is a viewer for automated active-site predictions for polypeptides

::DEVELOPER

Reveal Team

:: SCREENSHOTS

Reveal

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 Reveal

:: MORE INFORMATION

Citation

In Silico Biol. 2006;6(6):589-600.
Sequence-structure-function relation characterized in silico.
Brylinski M, Kochanczyk M, Konieczny L, Roterman I.

Jannotatix 0.8 – Sequence and Annotation Viewer

Jannotatix 0.8

:: DESCRIPTION

Jannotatix allows you to run algorithms that create predictions or annotations on a set of sequences. Examples are repeat finders, gene finders, splicing or binding site predictors. The results are returned in a common format and can be filtered, viewed and compared using a graphical interface. The main application at the moment is motif discovery on promotor sequences.

::DEVELOPER

Maximilian Haeussler

:: SCREENSHOTS

Jannotatix

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • Java

:: DOWNLOAD

 Jannotatix

:: MORE INFORMATION

AVIS 2 – AJAX viewer of Interactive Signaling Networks

AVIS 2

:: DESCRIPTION

AVIS is a Google gadget compatible web-based viewer of interactive cell signaling networks. AVIS is an implementation of AJAX (Asynchronous JavaScript with XML) with the usage of the libraries GraphViz, ImageMagic (PerlMagic) and overLib. AVIS provides web-based visualization of text-based signaling networks with dynamical zooming, panning and linking capabilities. AVIS is a cross-platform web-based tool that can be used to visualize network maps as embedded objects in any web page.

::DEVELOPER

Iyengar Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  AVIS

:: MORE INFORMATION

Citation

Berger SI, Iyengar R, and Ma’ayan A.
AVIS: AJAX Viewer of Interactive Signaling Networks.
Bioinformatics 2007 Sept 12

HyperTree 1.2.2 – Java Phylogenetic Tree Viewer

HyperTree 1.2.2

:: DESCRIPTION

HYPERTREE is a Java phylogenetic tree viewer, with a hyperbolic (‘fish-eye’) view and editing abilities that help in managing very large trees.

::DEVELOPER

kinase.com

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 HyperTree

:: MORE INFORMATION

Citation

Visualizing harge hierarchical clusters in hyperbolic space
J. Bingham, S Sudarsanam
Bioinformatics (2000) 16(7): 660-1

DisplayFam 1999 – Protein Familly Viewer

DisplayFam 1999

:: DESCRIPTION

DisplayFam browses protein families via the “Rich Family Description” format.

::DEVELOPER

Florence Corpet

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  DisplayFam

:: MORE INFORMATION

Citation

Browsing protein families via the “Rich Family Description” format
Bioinformatics Vol. 15, no 12 1999 pages 1020-1027
Florence CORPET, Jerome GOUZY and Daniel KAHN

Chemitorium 4.0 – Molecule Editor & 3D Chemical Structure Viewer

Chemitorium 4.0

:: DESCRIPTION

Chemitorium is Open-Source Molecule Editor and Viewer. Edit, compute, analyze and visualize chemical formulas. Formula Editor, 3D Rendering, Exporter, Video Module, Shaders, Antialiasing, Analysis Tools.

::DEVELOPER

Philipp Ruppel

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • NET Framework 2.0 oder higher
  • DirectX 9.0

:: DOWNLOAD

Chemitorium

:: MORE INFORMATION

N/A

Laj 070222 – Alignment Viewer

Laj 070222

:: DESCRIPTION

Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing additional information about particular regions.The program is written in Java in order to provide a graphical user interface that is portable across a variety of computer platforms; indeed its name stands for “Local Alignments with Java”. Currently it exists in two forms, a stand-alone application and a web-based applet, with slightly different capabilities.

::DEVELOPER

Cathy Riemer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

 Laj

:: MORE INFORMATION

Citation

Wilson MD, Riemer C, Martindale DW, Schnupf P, Boright AP, Cheung TL, Hardy DM, Schwartz S, Scherer SW, Tsui LC, Miller W, Koop BF.
Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5.
Nucleic Acids Res. 2001 Mar 15;29(6):1352-65.