Amino Acids

GETHGVBASE returns polymorphism data from the human genome variation db http://hgvbase.cgb.ki.seHGVDATA = gethgvbase(SNPID) reads in a %hgvbase web record fromEMBL and creates a structure DATA %containing fields correspondingto the hgvBase keywords.FIELDNAME DESCRIPTIONS: a complete %description...

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...

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

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

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

How do strong and weak acids differ? Use lab tools on your computer to find out! Dip the paper or the probe into solution to measure the pH, or put in the electrodes to measure the conductivity. Then see how concentration and strength affect pH. Can a weak acid solution have the same pH as a...


Platforms: Mac

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...


Platforms: Matlab

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

ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies...


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

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

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

ProDy is a free and open-source Python package for analyzing protein structural dynamics. It allows for quantitative analysis of heterogeneous experimental structural datasets and comparison with theoretically predicted conformational dynamics. The input for ProDy is the atomic coordinates of...


Platforms: *nix

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