Protein Similarity

The GMM returns the cluster centroid and cluster variances for a family of points if the number of clusters are predefined. The centroid and variance can then be passed to a Gaussian pdf to compute the similarity of a input query point with reference to given cluster. Platforms: Matlab

the stationary signal f(t)=cos(2*pi*5*t)+ cos(2*pi*10*t)+ cos(2*pi*20*t)+ cos(2*pi*50*t)having frequencies of 5,10, 20and 50 Hz at any given time instant.MATLAB program can be implemented to plot the stationary signal mentioned above:Clear... Platforms: Matlab

NCBI has an implementation of BLAST algorithm on their website at www.ncbi.nlm.nih.gov/BLAST, which is good if you want to query short DNA or protein sequence against various sequence databases. The problem arises when large sequences need to be BLAST'ed against a sequence database or against... Platforms: Matlab

The FindCore Toolbox (v. 1.0b)David Snyder and Gaetano Montelione, (C) 2010This Matlab Toolbox implements the FindCore algorithm described in Snyder, D.A.; Montelione, G.T. PROTEINS: Struct. Funct. Bioinformaticsm, 2005, 59: 673-86. Clustering algorithms for identifying core atom sets and for... Platforms: Matlab

MOTIFINFO = GIBBSMOTIFSAMPLER(SEQARRAY,MOTIFVECTOR,ALPHABET,OPTIONS) Searches for the motifs in a set of sequences via Gibbs sampling. seqArray is a cell vector of sequence strings. motifVector is a vector of uniformly-spaced motif widths you wish to optimize. The program iterates over these... Platforms: Matlab

PDBRead is a function that will read a Protein Data Bank file into a MATLAB structure.PDB_struct = PDBRead(filename) reads the file corresponding to filename and stores the information contained in this file in the PDB_struct. e.g. PDB_struct = PDBRead('PDBSilk.txt')The file that is being read by... Platforms: Matlab

Rsyso is a user interface created with Matlab dlT« to facilitate management control of monovariable linear models. Among the main functions that currently presents:d-deD? Find minimum realizations by different methods.d-deD? Conversions and main characteristics of the SISO model (transfer... Platforms: Matlab

It can be used to measure the total concentration of carbohydrate, protein, and lipid contents from solid wastes.The procedure was formulated to generate the detailed input required for the International Water Association (London, United Kingdom) Anaerobic Digestion Model number 1 (IWA-ADM1).The... Platforms: Matlab

Automated Text Review reviews texts from virtually any source and in virtually any way possible:Review... * Drupal code (using POTX). * Translation files. * *.tar.gz files that contain any of the above (using GNU Tar).Review methods * Blacklist review; filter out illegal words and phrases. *... Platforms: PHP

Taxonomy NCO uses Normalised Co-Occurrence analysis to look for relationships between terms in a freetagging vocabulary. This allows us to infer semantic relationships between terms.These modules have been developed at School of Everything. Configurable Normalised Co-occurrence Analysis of... Platforms: PHP

* jCompoundMapper provides popular fingerprinting algorithms for chemical graphs such as depth-first search fingerprints, shortest-path fingerprints, extended connectivity fingerprints, autocorrelation fingerprints (e.g. CATS2D), radial fingerprints (e.g. Molprint2D), geometrical Molprint, atom... Platforms: Mac

Seqlib is a Python module and application package for population genetics (and more). It allows processing, analyzing and simulating biological sequences. It is specifically designed for automated large-scale sequence analysis. Main features: * Fasta-centered input and output, format... 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

Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure We present Voroprot, an interactive cross-platform software tool that provides a unique set of capabilities for exploring geomeric features of protein structure. Voroprot allows... Platforms: Mac

A GUI program to create the plasmid database forms for BGME lab. This program presents user with a data entry form for entering plasmid information and automatically converts DNA sequence to protein, aligns it, and creates text output file. Platforms: Mac

The Ramachandran Plot Explorer really offers something new. The Ramachandran Plot Explorer is designed to make it easy to examine the conformation of a polypeptide - through the interactive Ramachandran plot (?Ya* -?Y? angles) and ?Ya*?-angle tool. Simply click on a residue, then drag the marker... Platforms: Mac

ProDy is a Python package designed for protein structural dynamics analysis. ProDy is developed by Ahmet Bakan and licensed under the GPLv3. New features and functions are constantly being added to ProDy. The following are the main features that are present and working fine: Protein structure... Platforms: Mac

For this ProfDistS provides a phylogenetic framework that uses individual RNA secondary structures in reconstructing phylogenies based on sequence-structure alignments - using Profile Neighbor Joining (PNJ) with manual or iterative and automatic profile definition. Moreover, ProfDistS can deal... Platforms: Mac

A Tool that manages Pathway Retrieval, Visualization and Analysis. Import a Gene or Protein Set from any Excel file. Find matching Pathways from KEGG. Integrate, visualze and analyze your Data in Seconds with interactive Force-directed Layout . Platforms: Mac

Stanford NER (also known as CRFClassifier) is a Java implementation of a Named Entity Recognizer. Named Entity Recognition (NER) labels sequences of words in a text which are the names of things, such as person and company names, or gene and protein names. The software provides a general... Platforms: Mac