Search Results for "algorithm" - Page 4

The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.

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.

BpMatch is an algorithm that, given 2 strings S and T, compute the maximum coverage of T using only subequence or reversed complemented subsequences of S, of minimum length l.

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.

Software tool (NEURON, Python, C++) based on the multi-agent Bee algorithm and aiming at multi-parametric optimization. 2 versions : - Link with NEURON (need download and install NEURON and NEURON-python) - Autonomous, with two types of neurones (Izhikevich and hodgkin huxley)

YaSeTo implements a modification of the widely used Sankoff-Algorithm for sequence/structure alignments of RNA sequences. It is suitable for genome-wide ncRNA gene finding, in case the ncRNA exhibits a conserved secondary structure.

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.

MTMP is a multi-threaded multiple pattern matching algorithm based on the Wu-Manber algorithm.

Algorithm Based Automatic Contiguation of Assembled sequences (ABACAS) is an integrated platform for quickly contiguating reference based assemblies.

Text2Genome is a set of scripts to extract nucleotide sequences from scientific articles and to map them to genomes and genes using a local alignment algorithm (BLAST/BLAT)

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

Juggernaut is a high throughput out of core sequence assembly algorithm. This program is very useful in assembly projects involving massive number of short reads which originate from high coverage of the genome.

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.

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.

This project implements an algorithm for segmenting protein sequences into smaller meaningful blocks. The method is based on the pure statistical approach and it uses an analogy between proteins and natural language.

Shape is a molecular conformation prediction program. It uses a genetic algorithm to efficiently search the conformational space of a biomolecule and then clusters the results. It is very simple to use.

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