BioWiki

Tools for bio

Useful softwares and web pages for your research. Please add software in this page !

Restriction enzymes

Plasmid map

PlasMapper

From web site — The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input. Plasmid sequences up to 20,000 bp may be annotated and displayed. Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format. PlasMapper supports an extensive array of display options.

This tool enables researchers to draw plasmid map quickly. For example, a map on the right hand was drawn by just inputing a sequence of pUC19 and clicking 'Graphic Map' button.

Reference → PubMed:15415271

Others

Draw plasmid maps on your web-browser. Quality of drawing lines and curves are substantially smooth by SVG.

Freeware for drawing plasmid maps.

Nucleic acid structure

mfold

The mfold is the well-known program that predicts the secondary structure of RNA and DNA.

SimTK RNA Folding

The ToRNADo is a one of the SimTK projects that can display the structure of RNA molecule.

Modeling softwares

<jmol ala.pdb.gz 100 100></jmol>

Freeware for windows.

Desktop dictionary

Point or select the word or phrase and 'Alt + click' to show the meaning.

Image manipulating

GIMP


commons

This is a freeware have been developing by open-source community. Almost platforms (Win/Mac/Linux) are supported.

Cytoscape(Freeware)

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

Podcast

Audio news from the following journals are available. You can import audio file to play PC or other audio players.