Webware & Free Downloads

Primer Design

Primer Generator - automated generator of primers for site-directed mutagenesis.

Web Primer

Operon Technologies - Oligo Analysis & Plotting Tool

Primer3 - pick primers from a DNA sequence

Consensus Degenerate Hybrid Oligonucleotide Primers - PCR primers designed from protein multiple sequence alignments

NetPrimer - Primers are analyzed for melting temperature and all secondary structures.

Sequence Analysis & Manipulation

REBASE - The Restriction Enzyme Database

Codon Usage Database

Gene Codes Corporation - international bioinformatics firm specializing in research software for DNA sequencing and analysis.

Entelechon - Free online bioinformatics tools: Protein backtranslation, Sequence inversion, Create a Codon Usage Table from a gene, Codon Usage table analysis, DNA Reader (reads DNA sequences aloud).

Webcutter - Analyze restriction maps of sequences.

DAN: DNA / RNA Melting Temperature

Molecular Visualization

RasMol Home Page

Chime - plugin do Netscape e IE para visualizar e interagir com com moleculas 3D de DNA e proteinas.

VMD - Visual Molecular Dynamics - molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

NAMD - parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Java Molecular Viewer - JMV - several molecular representations, multiple coloring styles, lighting controls, and stereoscopic rendering capabilities.

Protein Analysis

Swiss-PdbViewer - is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

Protein Sequence Analysis server - predicts probable secondary structures and folding classes for a given amino acid sequence.

TMpred - makes a prediction of membrane-spanning regions and their orientation.

TMHMM Server - Prediction of transmembrane helices in proteins