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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 ...
Algorithm and program for comparing primary biological sequence information, including DNA and protein sequences. Cross-platform: Public domain: National Center for Biotechnology Information: CP2K: Perform atomistic simulations of solid state, liquid, molecular and biological systems, written in Fortran 2003. Linux, macOS, Windows: GPL and LGPL
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
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.
"GLIMMER 3.0 has a start-site prediction accuracy of 99.5% for 3'5' matches where as GLIMMER 2.0 has 99.1% for 3'5' matches. GLIMMER 3.0 uses a new algorithm for scanning coding regions, a new start site detection module, and architecture which integrates all gene predictions across an entire genome." [5] Minimum description length
5 end Genomic end of the feature, with a 1-base offset. This is the same end coordinate as it is in 0-offset half-open sequence formats, like BED. [citation needed] 6 score Numeric value that generally indicates the confidence of the source in the annotated feature. A value of "." (a dot) is used to define a null value. 7 strand
In this first stage, the algorithm produces a multiple alignment, emphasizing speed over accuracy. This step begins by computing the k-mer distance for every pair of input sequences to create a distance matrix. UPGMA clusters the distance matrix to produce a binary tree. From this tree a progressive alignment is constructed, beginning with the ...