BLogo 1.0 – Visualization of Bias in Biological Sequences

BLogo 1.0

:: DESCRIPTION

Blogo is a web-based tool that detects and displays statistically significant position-specific sequence bias with reduced background noise. The over-represented and under-represented symbols in a particular position are shown above and below the zero line. When the sequences are in open reading frames, the background frequency of nucleotides could be calculated separately for the three positions of a codon, thus greatly reducing the background noise.

BLogo Online Version

::DEVELOPER

Dr. Wencheng Li (email lwcbio@yahoo.com.cn).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / Mac OsX
perl

:: DOWNLOAD

BLogo

:: MORE INFORMATION

Citation

Li W, Yang B, Liang S, Wang Y, Whiteley C, Cao Y, Wang X. (2008)
BLogo: A tool for visualization of bias in biological sequences.
Bioinformatics doi: 10.1093/bioinformatics/btn407.

PointCloudXplore 2.0 – Visualization and analysis of the data in PointCloud and Virtual Embryo Files

PointCloudXplore 2.0

:: DESCRIPTION

PointCloudXplore is a visualization tool for the PointCloud and Virtual Embryo data sets. It was developed to help biologists understand the relationship between gene expression patterns in three dimensions.

::DEVELOPER

the Berkeley Drosophila Transcription Network Project,

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX

:: DOWNLOAD

PointCloudXplore

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):296-309.
Visual exploration of three-dimensional gene expression using physical views and linked abstract views.
Weber GH, Rübel O, Huang MY, DePace AH, Fowlkes CC, Ker?nen SV, Luengo Hendriks CL, Hagen H, Knowles DW, Malik J, Biggin MD, Hamann B.

CluMa-GO 1.5 – Visualization of Mappings between the Gene Ontology and Cluster Trees

CluMa-GO 1.5

:: DESCRIPTION

CluMa-GO visualizes a large data set in the context of the Gene Ontology (GO) under consideration of a clustering of the data.

::DEVELOPER

The ISOVIS group

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux/ MacOSX
Java

:: DOWNLOAD

CluMa-GO

:: MORE INFORMATION

Citation

CluMa-GO: Bring Gene Ontologies and Hierarchical Clusterings Together
A. Kerren, I. Jusufi, V. Aleksakhin, and F. Schreiber
Extended Abstract, BioVis 11, Providence, RI, USA, 2011.

GLIEP – Navigation and Exploration of Interconnected Pathway Visualization

GLIEP

:: DESCRIPTION

GLIEP (Glyph-based Link Exploration of Pathways) helps to guide the navigation and exploration process of interconnected pathway visualization as well as providing insight into the overall interconnectivity.

::DEVELOPER

The ISOVIS group

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux/ MacOSX
Java
VANTED

:: DOWNLOAD

GLIEP

:: MORE INFORMATION

Citation

I. Jusufi, C. Klukas, A. Kerren, and F. Schreiber
Guiding the Interactive Exploration of Metabolic Pathway Interconnections
In Information Visualization, 2011. SAGE Publications

GRASP 2 -Visualization of Macromolecular Structures and Sequences

GRASP 2

:: DESCRIPTION

GRASP (Graphical Representation and Analysis of Structural Properties) is a program used for macromolecular structure and surface visualization. It contains a large number of new features and scientific tools: Enhanced GUI; Structure alignment and domain database scanning; A gaussian surface generator and new surface coloring schemes; Sequence visualization and alignment; Completed work can be stored in project files; Among the many objects that can be stored in a project file are views of the structure; defined subsets, surfaces; Direct printing to printers at full printer resolution.

::DEVELOPER

Barry Honig’s group

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

GRASP

:: MORE INFORMATION

Citation

Petrey, D. and Honig, B. (2003)
GRASP2: Visualization, Surface Properties, and Electrosttics of Macromolecular Structures and Sequences.
Methods in Enzymology. 374: 492-509

TAGster – Single or Multi-Population Tag SNPs Selection, Evaluation and Visualization

TAGster

:: DESCRIPTION

TAGster is a tool to select, evaluate and visualize LD tag SNPs for single or multiple populations

::DEVELOPER

Jack A. Taylor, M.D., Ph.D. , Zongli Xu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows /MacOsX

:: DOWNLOAD

TAGster

:: MORE INFORMATION

Citation:

Xu Z, Kaplan NL, Taylor JA.
TAGster: efficient selection of LD tag SNPs in single or multiple populations.
Bioinformatics. 2007 23:3254-5. Epub 2007 Sep 7

HaploVisual 0.04 – Haplotype data Visualization and Analyzation

HaploVisual 0.04

:: DESCRIPTION

The HaploVisual is a Java applet for haplotype data visualization and analyzation. It is intended to be used by both computer scientists (bioinformatics researchers) and biologists.

::DEVELOPER

Pasi Rastas

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux /MacOsX
Java

:: DOWNLOAD

HaploVisual

:: MORE INFORMATION

Citation

Ukkonen (2002),
“Finding founder sequences from a set of recombinants”
Lecture Notes in Computer Science Vol 2452, pp.277-286

SpotLink 1.0 – Proteomics tool for Organization and Visualization

SpotLink 1.0

:: DESCRIPTION

SpotLink is the tool for organizing proteomics raw data. The data includes 2D gel images, Mass Spectrometry (MS and MS/MS), protein expression profiles and etc.. The data is collected after a series of proteomics experiment and categorized by individual spot on gel.

::DEVELOPER

Primegens Team

:: SCREENSHOTS

:: REQUIREMENTS

Linux/Windows/MacOsX
Java

:: DOWNLOAD

SpotLink

:: MORE INFORMATION

Pedigree-Draw 6 – Genealogy Visualization

Pedigree-Draw 6

:: DESCRIPTION

Pedigree-Draw is a software that provides for creation, editing and drawing of pedigrees, or family trees, of human or non-human extended family lineages. It was developed originally for use in analyzing population data gathered for biomedical and genetic research. Although not designed as a genealogical database per se, the program can be used to collect and edit biographical data found in the course of family history research, as well as pictures of family members, and display or print those data in hierarchical diagrams suitable for publication. Output may also be saved in Portable Document Format (PDF) for distribution via the Internet, or posting on websites.

::DEVELOPER

Jurek Software

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX

:: DOWNLOAD

Pedigree-Draw

:: MORE INFORMATION

Medusa 3.0 – Visualization and Clustering Analysis of Biological Network

Medusa 3.0

:: DESCRIPTION

Medusa is a java standalone application for visualization and clustering analysis of biological networks in 2D. It is highly interactive and it supports weighted and multi-edged graphs where each edge between two bioentities can represent a different biological concept. Comparing to previous versions, it is currently enriched with a variety of layout and clustering methods for more intuitive visualizations. It is easy to integrate with web application since it is offered as an applet.

::DEVELOPER

Medusa Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

Medusa

:: MORE INFORMATION

Citation

Medusa: a simple tool for interaction graph analysis.
Hooper SD, Bork P
Bioinformatics. 2005 Dec 15; 21(24): 4432-3. Epub 2005 Sep 27; PubMed: 16188923.