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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 ...
BioJava is an open-source software project dedicated to provide Java tools to process biological data. [1] [2] [3] BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic ...
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 ...
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.
Mark Borodovsky (Russian: Марк Бородовский) is a Regents' Professor at the Join Wallace H. Coulter Department of Biomedical Engineering of Georgia Institute of Technology and Emory University and Director of the Center for Bioinformatics and Computational Genomics at Georgia Tech. [1] He has also been a Chair of the Department of Bioinformatics at the Moscow Institute of Physics ...
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 ...
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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.