XRNA 2.0 – Creation, Annotation & Display of RNA Secondary Structure Diagrams

XRNA 2.0

:: DESCRIPTION

XRNA is a Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams.XRNA provides editing tools for easy modification of publication quality secondary diagrams that can be either drawn manually, or through automatic generation. Other features include grouping, numbering and structure annotation. XRNA secondary structures may be saved in a native format, or exported as postscript for printing and further manipulation in programs such as Adobe Illustrator.

::DEVELOPER

RNA Center, UCSC

:: SCREENSHOTS


:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Perl

:: DOWNLOAD

XRNA

:: MORE INFORMATION

GEDS – Gene Expression Display Server

GEDS

:: DESCRIPTION

GEDS is an integrative platform to show human gene expressions in cancer types, normal tissues and cell lines for user input genes, miRNAs and proteins.

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Xia M, Liu CJ, Zhang Q, Guo AY.
GEDS: A Gene Expression Display Server for mRNAs, miRNAs and Proteins.
Cells. 2019 Jul 3;8(7):675. doi: 10.3390/cells8070675. PMID: 31277321; PMCID: PMC6678772.

matrix2png 1.2.2 – Visualization tool for Display of Matrix data

matrix2png 1.2.2

:: DESCRIPTION

matrix2png is a visualization tool for the display of matrix data.Matrix2png is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast, easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. Our group has found it useful for imaging all kinds of matrix-based data, not just microarray data.

::DEVELOPER

Pavlidis lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows with Cygwin

:: DOWNLOAD

 matrix2png

:: MORE INFORMATION

Citation

Pavlidis, P. and Noble W.S. (2003)
Matrix2png: A Utility for Visualizing Matrix Data.
Bioinformatics 19: 295-296

GView 1.7 – Display and Navigate Bacterial Genomes

GView 1.7

:: DESCRIPTION

GView is a java package used to display and navigate bacterial genomes. GView is useful for producing high-quality genome maps for use in publications and websites, or as a visualization tool in a sequence annotation pipeline. Users can interact with the genome using a powerful pan-and-zoom interface, or GView can write static images of a genome to a file. GView can draw a genome using either circular or linear layouts, with additional layout types planned for future release.

::DEVELOPER

Paul Stothard

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 GView

:: MORE INFORMATION

Citation:

Petkau A, Stuart-Edwards M, Stothard P, and Van Domselaar G.
Interactive microbial genome visualization with GView.
Bioinformatics 2010 26: 3125-3126.

Pairoscope 0.4.2 – Display of Paired End Reads

Pairoscope 0.4.2

:: DESCRIPTION

Pairoscope (formerly Yenta) was developed as a quick and simple way to generate diagrams indicating the relationship of paired end sequencing reads. It functions by displaying multiple genomic regions, their read depth at each base in the region and arcs within or between regions to indicate pairing information. Currently, Pairoscope supports the graphing of multiple regions, but they must be at different locations: the behavior of Pairoscope is undefined if attempting to graph the same region twice. It uses a bam file as input, and color codes the read pair graph to reflect different types of abnormally oriented reads. Individual reads are represented as vertical lines drawn at the genomic location where the read mapped.

::DEVELOPER

The Genome Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 Pairoscope

:: MORE INFORMATION

MOLDEN 5.8.2 – Package for Displaying Molecular Density

MOLDEN 5.8.2

:: DESCRIPTION

Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.

::DEVELOPER

MOLDEN team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

 MOLDEN

:: MORE INFORMATION

Citation

J Comput Aided Mol Des. 2000 Feb;14(2):123-34.
Molden: a pre- and post-processing program for molecular and electronic structures.
Schaftenaar G, Noordik JH.

Phy2HTML 1.0.1 – Display Phylogeny using only HTML and CSS

Phy2HTML 1.0.1

:: DESCRIPTION

Phy2HTML is a simple Python program that is designed to read a tree in Newick format and create a visualization of the tree for display in a webpage using only HTML and CSS.

::DEVELOPER

Michael S. Rosenberg’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

Phy2HTML

:: MORE INFORMATION

SAMStat 1.5.1 – Display Sequence Statistics for Next Generation Sequencing

SAMStat 1.5.1

:: DESCRIPTION

SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SAMStat

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 1;27(1):130-1. doi: 10.1093/bioinformatics/btq614. Epub 2010 Nov 18.
SAMStat: monitoring biases in next generation sequencing data.
Lassmann T1, Hayashizaki Y, Daub CO.

IBDfinder 20121128 – Visual display of homozygous regions in SNP data files

IBDfinder 20121128

:: DESCRIPTION

IBDFinder aids the identification of regions of Identity By Descent (IBD) in inbred individuals, by plotting and collating runs of homozygous SNP genotypes, ordered by physical or genetic distance.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

IBDfinder

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

  IBDfinder

:: MORE INFORMATION

Citation

Hum Mutat. 2009 Jun;30(6):960-7. doi: 10.1002/humu.20974.
IBDfinder and SNPsetter: tools for pedigree-independent identification of autozygous regions in individuals with recessive inherited disease.
Carr IM, Sheridan E, Hayward BE, Markham AF, Bonthron DT.

AgileVariantViewer 20120105 – Allows Sequence Variants to be interactively Displayed and Filtered

AgileVariantViewer 20120105

:: DESCRIPTION

AgileVariantViewer allows sequence variants to be interactively displayed and filtered.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

AgileVariantViewer

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 AgileVariantViewer

:: MORE INFORMATION