Amino Acid Sequence

Structure is a screensaver for Mac OS X that draws on the National Center for Biotechnology Information's protein databases to display beautiful 3D protein structures on your screen. It ships with about ten sample structures and via the Internet has seamless access to a database of tens of... Platforms: Mac

MPEx is a small, easy to use application designed to help you explore the topology and other features of membrane proteins by means of hydropathy plots based upon thermodynamic and biological principles. The program is based on sliding-window analysis that represents an amino acid sequence as a... Platforms: Windows

The sixth MATLAB Programming Contest, Protein, will run from November 6-13, 2002.This contest concerns a very simplified two-dimensional version of the protein folding problem. Given the amino acid sequence of a simplified protein, your job is to determine a final "optimally folded"... Platforms: Matlab

The Nucleic Acid Nomenclature is a Dashboard widget that displays general information on nucleic acids (symbol, meaning, complement and origin of designation) conformed with the IUPAC-IUB recommandations. Platforms: Mac

The Nucleic Acid Table widget displays useful information on nucleic acids including molecular weigth and composition. Platforms: Mac

The usual way to demonstrate saturation in nucleotide sequences is to plot the fraction of differences between sequences against the evolutionary distance separating them. When the number of observed differences, for example for the fraction of third codon positions, no longer increases with... Platforms: Windows

A Molecular Biology software that provides tools with an intuitive interface to assists you in DNA cloning, sequence analysis and visualization. Serial Cloner 2.1 handles Features/Annotations and now allows to define, import and export, customized lists of Features. User can annotate any sequence... Platforms: Mac

A set of programs for multiple sequence alignment and analysis. The programs use an expandable user interface which allows the addition of external analysis functions without any rewriting of code. The system supports several data types, nucleic and amino acid sequences, text, and masking... Platforms: Mac

OligoLocator is a simple, Java based application designed to identify the position of oligonucleotides within nucleic acid sequences with varying degrees of mismatch between the two. Platforms: Windows

Swiss-PdbViewer (aka DeepView) 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... Platforms: Mac

Bio::Tools::Run::PiseApplication::charge is a Perl module. Bio::Tools::Run::PiseApplication::charge Bioperl class for: CHARGE Protein charge plot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/charge.html for available values): charge (String) init... Platforms: *nix

Bio::Tools::CodonTable is a bioperl codon table object. SYNOPSIS # This is a read-only class for all known codon tables. The IDs are # the ones used by nucleotide sequence databases. All common IUPAC # ambiguity codes for DNA, RNA and animo acids are recognized. # to use use... Platforms: *nix

The ProtParam widget computes physico-chemical parameters for your protein sequences at ExPASy. You just have to type or paste your sequence in the input field. Platforms: Mac

The BLAST widget provides a quick access to the Basic Local Alignment Search Tool at NCBI. You just have to type or paste your sequence and to select the program to be used. Platforms: Mac

Translated BLAST Widget provides a quick access to the Translated Basic Local Alignment Search Tool at NCBI. You just have to type or paste your sequence and to select the program to be used. Platforms: Mac

Protein BLAST Widget provides a quick access to the Protein Basic Local Alignment Search Tool at NCBI. You just have to type or paste your sequence and to select the program to be used. Platforms: Mac

Nucleotide BLAST Widget provides a quick access to the Nucleotide Basic Local Alignment Search Tool at NCBI. You just have to type or paste your sequence and to select the program to be used. Platforms: Mac

A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.) Platforms: Windows, Mac, Linux

The Entrez Widget provides a quick access to the NCBI Databases. You just have to enter your search terms and the result will be displayed in a new browser window. Platforms: Mac

The DNA Molar Converter widget is a Dashboard widget that allows to perform molar conversions for nucleic acids according to size. Platforms: Mac