mapscape – Visualization tool for spatial Clonal Evolution

mapscape

:: DESCRIPTION

MapScape is a visualization tool for spatial clonal evolution.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

mapscape

:: MORE INFORMATION

PIVOT 2.0 – Protein Interactions VisualizatiOn Tool

PIVOT 2.0

:: DESCRIPTION

PIVOT (Protein Interactions VisualizatiOn Tool) is a Java-based tool, for visualizing protein-protein interactions. It is rich in features that help the users navigate and interpret the interactions map, as well as graph-theory algorithms for easily connecting remote proteins to the displayed map.PIVOT is not limited to the data present in any database, but instead allows the users to create their own dataset, by importing any available lists of interactions and combining them together. PIVOT is currently configured to work with proteins from four different species (human, yeast, drosophila and mouse), and present functional annotations, designations of homologs from the four species, and links to information pages. The protein data is stored in an MS-Access file, easily modifiable by the users to enter their own data.

::DEVELOPER

PIVOT team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PIVOT

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Feb 12;20(3):424-5. Epub 2004 Jan 22.
PIVOT: protein interacions visualizatiOn tool.
Orlev N1, Shamir R, Shiloh Y.

Circleator 1.0.0 – Perl-based Genome-associated data Visualization Tool

Circleator 1.0.0

:: DESCRIPTION

Circleator is a Perl application that generates circular figures of genome-associated data. It leverages BioPerl to support standard annotation and sequence file formats and produces publication-quality SVG output.

::DEVELOPER

Jonathan Crabtree <jonathancrabtree@gmail.com> @ the Institute for Genome Sciences in the University of Maryland’s School of Medicine.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Perl
  • BioPerl

 Circleator

:: MORE INFORMATION

Citation

Circleator: Flexible Circular Visualization of Genome-Associated Data with BioPerl and SVG.
Crabtree J, Agrawal S, Mahurkar A, Myers GS, Rasko DA, White O.
Bioinformatics. 2014 Jul 29. pii: btu505.

SinicView 1.0.3 – Large-scale Alignment Visualization Tool

SinicView 1.0.3

:: DESCRIPTION

SinicView, (for Sequence-aligning INnovative and Interactive Comparison VIEWer), allows the user to efficiently compare and evaluate assorted nucleotide alignment results obtained by different tools. SinicView calculates similarity of the alignment outputs under a fixed window using the sum-of-pairs method and provides scoring profiles of each set of aligned sequences. The user can visually compare alignment results either in graphic scoring profiles or in plain text format of the aligned nucleotides along with the annotations information. We illustrate the capabilities of our visualization system by comparing alignment results obtained by MLAGAN, MAVID, and MULTIZ, respectively.

::DEVELOPER

Arthur Shih Lab , Academia Sinica, Taiwan

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX/Linux
  • java 

:: DOWNLOAD

 SinicView

:: MORE INFORMATION

Citation:

Shih AC, Lee DT, Lin L, Peng CL, Chen SH, Wu YW, Wong CY, Chou MY, Shiao TC, Hsieh MF.
SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools
BMC Bioinformatics 2006, 7:103 doi:10.1186/1471-2105-7-103

DROMPA 2.6.4 – Peak-calling and Visualization Tool for Multiple ChIP-seq Data

DROMPA 2.6.4

:: DESCRIPTION

DROMPA (DRaw and Observe Multiple enrichment Profiles and Annotation) is cost-effient program for peak-calling and visualization for ChIP-seq analysis. DROMPA outputs the protein binding profile map (ChIP-reads distribution and ChIP/control enrichment profile) with genomic annotation specified in pdf or png format, which can be easily handled and processed by users with little bioinformatics background. DROMPA has an associated program named parse2wig, which preprocesses the map file into wig files. This two-step procedure can drastically reduce the computational memory and time required, which makes enable to analyze large-scale ChIP-seq data (e.g., more than 10 human samples and/or multiple executions for each sample with trial-and-error) on a conventional desktop computer.

::DEVELOPER

Ryuichiro NAKATO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

DROMPA

:: MORE INFORMATION

Citation:

Genes Cells. 2013 Jul;18(7):589-601. doi: 10.1111/gtc.12058.
DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.
Nakato R, Itoh T, Shirahige K.

Strainer 0.9.4b – Multi-platform Visualization tool for Metagenomics Data

Strainer 0.9.4b

:: DESCRIPTION

 Strainer is a multi-platform visualization tool for metagenomics data. It allows the user to easily browse the variation present in shotgun sequence data from non-clonal samples.

::DEVELOPER

Jill Banfield

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows with cygwin/MacOsX
  • Java

:: DOWNLOAD

 Strainer

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Oct 17;8:398.
Strainer: software for analysis of population variation in community genomic datasets.
Eppley JM, Tyson GW, Getz WM, Banfield JF.

HaploGeneMapper 1.0 – Genomic Proximity of Haplo Insufficient Genes Visualization tool

HaploGeneMapper 1.0

:: DESCRIPTION

HaploGeneMapper is a tool to visualise the genomic proximity of haploinsufficient genes to segmental duplications on a chromosome-by-chromosome basis. Corresponding pairs of segmental duplications, which may be subject to non-allelic homologous recombination, can be highlighted using the cursor. Similarly, the names of haploinsufficient genes and segmental duplications can be displayed by hovering the cursor over them.

::DEVELOPER

HaploGeneMapper team

:: SCREENSHOTS

HaploGeneMapper

:: REQUIREMENTS

  • Linux /MacOsX/ Windows
  • Java

:: DOWNLOAD

 HaploGeneMapper

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2008 Nov;16(11):1350-7. doi: 10.1038/ejhg.2008.111.
Identification of human haploinsufficient genes and their genomic proximity to segmental duplications.
Dang VT, Kassahn KS, Marcos AE, Ragan MA.

RnallViewer 1.0.1 – RNA Analysis Visualization Tool

RnallViewer 1.0.1

:: DESCRIPTION

RnallViewer is an RNA analysis and visualization tool that combines information and processing from various command-line tools in an intuitive graphical user interface (GUI). Rnall is used for generating RNA structure predictions, which can be automatically sent to Naview, plt22ps, and Ghostscript for visualization. Annotation information can be included, parsed with the help of BioJava. RnallViewer’s panelling system allows much of this information to be displayed simultaneously, and comprehensive searching methods allow quick access to specific regions based on annotation and position criteria in the format of NCBI ptt format

::DEVELOPER

Systems Biology Laboratory, College of Veterinary Medicine,Mississippi State University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

RnallViewer

:: MORE INFORMATION

Citation

Wan, X.-F., P. P. Dempsey, and D. Xu. 2008.
RnallViewer: A tool for RNA local secondary structure prediction, localization, and visualization.
International Journal of Computational Science, Special Issue on Bioinformatics and Computational Biology, 2(5): 607-612.

AStalavista 3.2 – Alternative Splicing Transcriptional Landscape Visualization tool

AStalavista 3.2

:: DESCRIPTION

AStalavista (the Alternative Splicing Trascriptional Landscape Visualization Tool) retrieves all alternative splicing events from generic transcript annotations.

::DEVELOPER

Genome BioInformatics Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • Java 

:: DOWNLOAD

 AStalavista

:: MORE INFORMATION

Citation

Sammeth M, Foissac S, Guigó R (2008)
A General Definition and Nomenclature for Alternative Splicing Events.
PLoS Comput Biol 4(8): e1000147.