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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 ...
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.
Printer-friendly PDF version of the Algorithms Wikibook. Licensing Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License , Version 1.2 or any later version published by the Free Software Foundation ; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
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 ...
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
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.
General GFF3 structure Position index Position name Description 1 seqid The name of the sequence where the feature is located. 2 source The algorithm or procedure that generated the feature.
Does linear programming admit a strongly polynomial-time algorithm? (This is problem #9 in Smale's list of problems.) How many queries are required for envy-free cake-cutting? What is the algorithmic complexity of the minimum spanning tree problem? Equivalently, what is the decision tree complexity of the MST problem?