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.

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.

...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.

LAITOR is a text mining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries.

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.