Search Results for "algorithm" - Page 3

MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/

We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.

This is a Python program based on the NegEx algorithm that detects the polarity of the clinical evidence in clinical random trials. If you use this code please cite this paper: P. Davis-Desmond and Diego Mollá. Detection of Evidence in Clinical Research Papers (2012). Australasian Workshop On Health Informatics and Knowledge Management (HIKM 2012), Melbourne, Australia. http://www.ics.mq.edu.au/~diego/publications/hikm12.pdf

CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.

BIL++ is a set of standalone C++ packages for data processing in Bioinformatics (Graph mining, Bayesian networks, Genetic algorithm, Discretization, Gene expression data analysis, Hypothesis testing).

Foad is an open source software which receive an EKG Signal from scanner, WFDB database or heart sensors. Finding patient disease started by taking Fourier transform (FFT) from input signal and extract a single cycle. Based on some heuristic algorithm the most important feature like P , Q , R , S , T captured and feed to trained neural network. and so the final decision made by CNN library. As mentioned before this software also capable do some image processing on scanned paper to lower the final costs.

This library is a lightweight implementation of genetic algorithm, contains the most popular types of chromosomes and the basic algorithms for selection, elitism, crossing and mutation.

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74

BorderFlow implements a general-purpose graph clustering algorithm. It maximizes the inner to outer flow ratio from the border of each cluster to the rest of the graph.

CheMecher is a fully-featured chemical simulator that supports an arbitrary number of reaction steps and chemical species. Uses the Runge-Kutta algorithm for numeric solutions.

Multi-functional batch sequence aligner incorporating Needleman-Wunsch, Smith-Waterman and Oommen-Kashyap algorithms along with compound alignment of secondary sequences.

CEGA is a highly extendable layout plugin for Cytoscape based on an Evolutionary Algorithm. In contrast to other layout algorithms, CEGA lets users decide which features are important for the visualization of their graphs.

D-finder is a bioinformatic search algorithm for the identification of D-sites in JNK interacting proteins. The algorithm is a combination of pattern matching and a hidden markov model (HMM) based on a training set of known JNK D-sites.

This is an global sequence alignment tool (GSA) created using visual basic 6.0. In this software, Needleman & Wunsch algorithm is used.

TaxonFinder is an application that annotates taxon found in literature. The application harnesses a hybrid algorithm that is necessarily a combination of morphological analysis, dictionary lookup and Levenstein Distance algorithm.

An efficient implementation of the Smith-Waterman algorithm that takes advantage of SIMD instruction sets in modern CPUs. The Smith-Waterman algorithm is used for sequence alignment in bioinformatics.

This is a reference implementation of snoBAC, a Bayesian Classifier designed to predict box H/ACA snoRNAs in Caenorhabditis nematode genomes. For details of algorithm and data, see Wang and Ruvinsky (2009) RNA in press.

ChIPOTle is a peak-finding algorithm used to analyze ChIP-chip microarray data

Java GUI to analyze one (or more, in batch mode) datasets with several feature selection methods at the same time and also performing an "ensemble" analysis. It can be easily extended to include any feature selection algorithm.

A polynomial-time algorithm for constructing level-2 phylogenetic networks from dense sets of rooted triplets.

The program predicts the optimal folding of all consecutive substrings of length L of an RNA sequence of length N in O(NL) time. The algorithm is based on two papers: Wexler, Zilberstein, Ziv-Ukelson (2007), and Horesh, Wexler, Ziv-Ukelson ,Unger (2008)

Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.

The software implements a fast optimal co-folding of pairs of RNA sequences. The algorithm is described in details in the paper "A faster algorithm for RNA co-folding" by Ziv-Ukelson, Gat-Viks, Wexler, and Shamir.

A novel algorithm to layout the contigs with more than one reference genomes at a time using global searches

TACS (Trust Ant Colony System) is a Trust model for P2P, Ad-hoc and Wireless Sensor networks (also valid for multi-agent systems) based on the bio-inspired algorithm ACS (Ant Colony System).