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  2. GeneMark - Wikipedia

    en.wikipedia.org/wiki/GeneMark

    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 ...

  3. Gene prediction - Wikipedia

    en.wikipedia.org/wiki/Gene_prediction

    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.

  4. List of gene prediction software - Wikipedia

    en.wikipedia.org/wiki/List_of_gene_prediction...

    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 ...

  5. General feature format - Wikipedia

    en.wikipedia.org/wiki/General_feature_format

    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.

  6. SEA-PHAGES - Wikipedia

    en.wikipedia.org/wiki/SEA-PHAGES

    This algorithm is utilized by DNA Master, and there is an online version that can be used to cross-reference the calls made by the software. [3] It shows definitive tRNAs and tmRNAs within a genome by looking for very specific sequences that would fold into the distinctive cloverleaf secondary structure. [ 7 ]

  7. MAFFT - Wikipedia

    en.wikipedia.org/wiki/MAFFT

    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

  8. Mark Borodovsky - Wikipedia

    en.wikipedia.org/wiki/Mark_Borodovsky

    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 ...

  9. List of numerical libraries - Wikipedia

    en.wikipedia.org/wiki/List_of_numerical_libraries

    It implements a number of genetic, fuzzy logic and machine learning algorithms with several architectures of artificial neural networks with corresponding training algorithms. LGPLv3 and partly GPLv3. ALGLIB is an open source numerical analysis library with C# version. Dual licensed: GPLv2+, commercial license.

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