Search Results for "gene"

This package includes a few programs for rapid functional annotation for metagenomic sequences, including, 1) Gene prediction by FragGeneScan; 2) Similarity search by RAPSearch2; 3) Functional annotation in GO (Gene Ontology) and EC (Enzyme Commission) based on similarity search results; 4) From EC to metabolic pathway reconstruction by MinPath. Inputs: Just sequencing reads (or assemblies) Outputs: Protein-coding genes (or gene fragments); similarity search; functional annotations (in GO and EC); metabolic pathways.

DEBay: Deconvolution of Ensemble through Bayes-approach DEBay estimates cell type-specific gene expression by deconvolution of quantitative PCR data of a mixed population. It will be useful in experiments where the segregation of different cell types in a sample is arduous, but the proportion of different cell types in the sample can be measured. DEBay uses the population distribution data and the qPCR data to calculate the relative expression of the target gene in different cell types in the sample. ...

The source code has been migrated and is now hosted on Github: https://github.com/jenetics/jenetics Jenetics is an advanced Genetic Algorithm, Evolutionary Algorithm and Genetic Programming library, respectively, written in modern day Java. It is designed with a clear separation of the several algorithm concepts, e. g. Gene, Chromosome, Genotype, Phenotype, Population and fitness Function. Jenetics allows you to minimize or maximize the given fitness function without tweaking it. In contrast to other GA implementations, the library uses the concept of an evolution stream (EvolutionStream) for executing the evolution steps. Since the EvolutionStream implements the Java Stream interface, it works smoothly with the rest of the Java Stream API. ...

GAKNN is a data mining software for gene annotation data. GAKNN is built with k- Nearest Neighbour algorithm optimized by the genetic algorithm. Gene annotation datasets saved under .csv or .arff formats with Gene Ontology or FunCat categorization can use GAKNN to predict gene functions.

...The genetic algorithm engine supports various mutation rates, ranked parental selection, stochastic sampling parental selection, cyclic crossover, crossover at each gene, cloning the best individual each generation, and creating random individuals each generation. To use the genetic algorithm engine to search for a different problem's solution, one needs to program a fitness function, the project settings, and a few virtual functions.

...This may be useful to reverse-engineer human constructs like electronic equipment, manufactured machines, or bureaucratic hierarchies; but also to decompose natural constructs like gene-relation or protein-relation nets.

GEP is an evolutionary algorithm for function finding. This framework is a powerful way of expressing and coding genetic-like structures and quickly finding solutions through evolution by common genetic operators.

The Gene Expression Programming Framework in Java. It separates the process of evolution from the process of interpretation of the chromosome, allowing the use of various schemes in the chromosome.

Conrad is both a high performance Conditional Random Field engine which can be applied to a variety of machine learning problems and a specific set of models for gene prediction using semi-Markov CRFs.