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GeneMark is a generic name for a family of ab initio gene prediction algorithms and software programs developed at the Georgia Institute of Technology in Atlanta.Developed in 1993, original GeneMark was used in 1995 as a primary gene prediction tool for annotation of the first completely sequenced bacterial genome of Haemophilus influenzae, and in 1996 for the first archaeal genome of ...
In bioinformatics, MAFFT (multiple alignment using fast Fourier transform) is a program used to create multiple sequence alignments of amino acid or nucleotide sequences. . Published in 2002, the first version used an algorithm based on progressive alignment, in which the sequences were clustered with the help of the fast Fourier transfo
Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to ab initio gene finding, in which the genomic DNA sequence alone is systematically searched for certain tell-tale signs of protein-coding genes.
Its name stands for Prokaryotic Dynamic Programming Genefinding Algorithm. It is based on log-likelihood functions and does not use Hidden or Interpolated Markov Models. Prokaryotes, Metagenomes (metaProdigal) [4] AUGUSTUS: Eukaryote gene predictor: Eukaryotes [5] BGF Hidden Markov model (HMM) and dynamic programming based ab initio gene ...
The MOEA Framework is an open-source evolutionary computation library for Java that specializes in multi-objective optimization. It supports a variety of multiobjective evolutionary algorithms (MOEAs), including genetic algorithms, genetic programming, grammatical evolution, differential evolution, and particle swarm optimization. As a result ...
GFF3 addresses this and other deficiencies. For example, it supports arbitrarily many hierarchical levels, and gives specific meanings to certain tags in the attributes field. The GTF is identical to GFF, version 2. [1]
GEP4J – GEP for Java Project Created by Jason Thomas, GEP4J is an open-source implementation of gene expression programming in Java. It implements different GEP algorithms, including evolving decision trees (with nominal, numeric, or mixed attributes) and automatically defined functions. GEP4J is hosted at Google Code.
In fact, runtime systems for modern programming languages (such as Java and the .NET Framework) usually use some hybrid of the various strategies that have been described thus far; for example, most collection cycles might look only at a few generations, while occasionally a mark-and-sweep is performed, and even more rarely a full copying is ...