Tag: Diagram

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

Pandora 4.2 – Protein ANnotation Diagram ORiented Analysis

Pandora 4.2

:: DESCRIPTION

PANDORA is a web server which functions as a platform for the advanced biological analysis of sets of genes, proteins, or proteolytic peptides.

::DEVELOPER

The Sudarsky Center for Computational Biology – The Hebrew University of Jerusalem

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W84-9. doi: 10.1093/nar/gkq320. Epub 2010 May 5.
PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations.
Rappoport N1, Fromer M, Schweiger R, Linial M.

DrawCoil 1.0 – Produce Coiled-coil Helical Wheel Diagrams

DrawCoil 1.0

:: DESCRIPTION

DrawCoil is a web-based program for creating coiled-coil helical wheel diagrams.

::DEVELOPER

Grigoryan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

  DrawCoil

:: MORE INFORMATION

Citation:

G. Grigoryan and A. E. Keating,
“Structural Specificity in Coiled-coil Interactions”,
Current Opinion in Structural Biology, 18(4): 477-483, 2008

SeDD 20141028 – Sequence Diversity Diagram

SeDD 20141028

:: DESCRIPTION

SeDD is designed for comparative analysis of multiple sequence alignments. The amino acid positions are laid horizontally on the x-axis. Amino acid residues and their groupings are laid on the y-axis. The grouping of amino acids based on their structure and the general chemical characteristics is visually enhanced with horizontal gaps. On this grid layout, a flow diagram is drawn to represent sequence alignment frequency and each sample is color-coded. The line weight represents the relative frequency of residues at the two consecutive positions with respect to the total number of sequences. By linking two adjacent positions, it visualizes the sequential frequency and co-occurrence between two adjacent positions. By overlaying two samples, both the conserved and diverse positions are studied in a single figure.

::DEVELOPER

Bioinformatics Research Group, Belgium

:: SCREENSHOTS

SeDD

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Java

:: DOWNLOAD

 SeDD

:: MORE INFORMATION

MapMan 3.6.0RC1 – Displays large datasets onto Diagrams of Metabolic Pathways

MapMan 3.6.0RC1

:: DESCRIPTION

MapMan is a user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MapMan

:: MORE INFORMATION

Citation

Thimm O, Blaesing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY and M Stitt (2004)
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Plant J. 37(6):914-39.

PathwayExplorer 3.0.2 – Construction of Biological Pathway Diagrams

PathwayExplorer 3.0.2

:: DESCRIPTION

The PathwayExplorer is an easy to use and platform independent interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them. This novel drawing tool integrates the possibilities of charting elements with different attributes (size, color, labels), drawing connections between elements in distinct characteristics (color, structure, width, arrows), as well as adding links to molecular biology databases, promoter sequences, information on the function of the genes or gene products, and references. The result of the editing process is a PNG (portable network graphics) file for the images and XML (extended markup language) file for the appropriate links. Further it is possible to map expression datasets to the pathways by using gene RefSeq ids. It is also possible to use a SOAP interface to access the pathways online.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Oracle / PostgreSQL / MySQL

:: DOWNLOAD

 PathwayExplorer

:: MORE INFORMATION

Citation

Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z.
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways.
Nucleic Acids Res. 33: W633-W637 (2005)

PEDIGREE VIEWER 6.5b – Draw & Manipulate Pedigree Diagrams

PEDIGREE VIEWER 6.5b

:: DESCRIPTION

PEDIGREE VIEWER reads your simple data file and displays the full pedigree structure on the screen. Each animal is represented by its identity, or its name, or by its value for any of the traits in the data file. You can display a large pedigree of thousands of animals all on the screen at the one time. Data are overlapped on the screen for such large pedigrees, but in one mode an individual’s information is highlighted as the mouse cursor passes over. You can ask to find an animal(s) by identity, or by merit or merit range for a given trait.

::DEVELOPER

by Brian and Sandy Kinghorn.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PEDIGREE VIEWER

:: MORE INFORMATION

Citation

Brian P Kinghorn
An algorithm for efficient constrained mate selection
Genetics Selection Evolution 2011, 43:4