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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 ...
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.
Trilinos is an effort to develop algorithms and enabling technologies for the solution of large-scale, complex multi-physics engineering and scientific problems. It is a collection of packages . Template Numerical Toolkit (TNT) linear algebra software in the public domain and entirely in the form of headers, from NIST.
The modENCODE project hosts an online GFF3 validation tool with generous limits of 286.10 MB and 15 million lines. The Genome Tools software collection contains a gff3validator tool that can be used offline to validate and possibly tidy GFF3 files. An online validation service is also available.
A combination of three small LCGs, suited to 16-bit CPUs. Widely used in many programs, e.g. it is used in Excel 2003 and later versions for the Excel function RAND [8] and it was the default generator in the language Python up to version 2.2. [9] Rule 30: 1983 S. Wolfram [10] Based on cellular automata. Inversive congruential generator (ICG) 1986
MFEM is a free, lightweight, scalable C++ library for finite element methods. Origin, a software package that is widely used for making scientific graphs. It comes with its own C/C++ compiler that conforms quite closely to ANSI standard. PAW is a free data analysis package developed at CERN.
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