Amino Acids

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"...

Some of the logic from this program was provided from PDBRead.m by Sachin Nikumbh. The version I made is a trimmed down version of it that only outputs the data from one atom type (protein by default), and formats it as convenient cell variables. For smaller PDB files, the time difference between...

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" configuration. Each potential arrangement of the protein sequence is associated with an energy...


Platforms: Matlab

This application is an interactive simulation of gene expression that allows the user to: Explore a sample gene: Explore the correspondence between DNA, pre-mRNA, mature mRNA, and protein Map the functional elements of a gene. Create mutations in a gene and explore their effects. Design...


Platforms: Mac

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

Clusterfunc is a simple and fast method for Clustering functionally divergent genes by Functional Category. Changes in protein structure and function are reflected at the level of amino acid sequence. This principle suggests that functional divergence - changes in protein function, for instance...


Platforms: Mac

What is snpEff? It's a variant effect predictor tool, it predicts the effect of genetic variations (SNPs, insertions, deletions and MNPs). Release Candidate 1 Take a look at all the new features added Database download command, e.g. "java -jar snpEff.jar download GRCH37.64" RefSeq annotations...


Platforms: Mac

The Nucleic Acid Modeling Tool(NAMOT) is a program to allow users to manipulate molecular models of nucleic acids based on a set of reduced co-ordinates developed at Los Alamos National Laboratory and the Max Planck Institute for Biophysical Chemistry.


Platforms: *nix

FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison. Features . Comparison of Genomes, protein and nucleic acid sequences...


Platforms: *nix

nebseq is a Python module for basic biological sequence manipulations. Import as usual >>> import nebseq Reverse complements The only note here is that revcomp does not check the input sequence to see if it looks like DNA or RNA. >>> nebseq.revcomp('ACGT') 'ACGT' >>>...


Platforms: *nix

This highly functional and easy to use Scientific Calculator is a must for science students. The main calculator has over 40 functions while an extensive number of utilities, tools and science data reference systems can be called. The calculator contains one of the most extensive measurement...


Platforms: Windows, Windows 8, Windows 7, Windows Server

Support streaming the video and audio content stream to Wowza Media Server, Adobe Media Server. Then you may deliver a live stream at the same time to Adobe Flash Player, Apple iOS devices (iPhone, iPad, or iPod touch) or Apple TV digital media extender, Roku and Amino set-top boxes, Microsoft...


Platforms: Windows, Windows 7

Support streaming the video and audio content stream to Wowza Media Server, Adobe Media Server. Then you may deliver a live stream at the same time to Adobe Flash Player, Apple iOS devices (iPhone, iPad, or iPod touch) or Apple TV digital media extender, Roku and Amino set-top boxes, Microsoft...


Platforms: Windows, Windows 7

Check if the food you buy contains additives dangerous to your health. Have you ever wondered what all of those e-numbers actually mean? This free application contains list of food additives by e-number or by name telling you which to avoid. Also additives that children, asthmatics, vegetarians...


Platforms: Windows