Suffix Tree
Mostrando 1-7 de 7 artigos, teses e dissertações.
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1. Perseus:uma nova técnica para tratar árvores de sufixo persistentes / Perseus: a novel technique to handle persistent suffix trees
Due to the technological advances in molecular biology laboratories, biological databases are extremely voluminous and tend to become more voluminous as data on new genome organisms are available. This introduces the challenge of searching nucleotide sequences efficiently. The suffix tree is an access method used for several applications that search for thes
Publicado em: 2009
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2. Filtros para a busca e extração de padrões aproximados em cadeias biológicas / Filter Algorithms for Approximate Patterns Matching and Extraction from Biological Strings
Esta dissertação de mestrado aborda formulações computacionais e algoritmos para a busca e extração de padrões em cadeias biológicas. Em particular, o presente texto concentra-se nos dois problemas a seguir, considerando-os sob as distâncias de Hamming e Levenshtein: a) como determinar os locais nos quais um dado padrão ocorre de modo aproximado em
Publicado em: 2008
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3. Busca e recuperaÃÃo de componentes de software utilizando agrupamento de componentes
The development of software with reuse is an approach that can be used to achieve two main benefits: (1) increase in productivity of software projects and (2) improvements in the final quality of the products. The software reuse approach can be instantiated through the strategy of development based in software components. According to this strategy, large so
Publicado em: 2008
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4. Alignment of whole genomes.
A new system for aligning whole genome sequences is described. Using an efficient data structure called a suffix tree, the system is able to rapidly align sequences containing millions of nucleotides. Its use is demonstrated on two strains of Mycoplasma tuberculosis, on two less similar species of Mycoplasma bacteria and on two syntenic sequences from human
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5. SA-Search: a web tool for protein structure mining based on a Structural Alphabet
SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such
Oxford University Press.
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6. SSAHA: A Fast Search Method for Large DNA Databases
We describe an algorithm, SSAHA (Sequence Search and Alignment by Hashing Algorithm), for performing fast searches on databases containing multiple gigabases of DNA. Sequences in the database are preprocessed by breaking them into consecutive k-tuples of k contiguous bases and then using a hash table to store the position of each occurrence of each k-tuple.
Cold Spring Harbor Laboratory Press.
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7. Fast algorithms for large-scale genome alignment and comparison
We describe a suffix-tree algorithm that can align the entire genome sequences of eukaryotic and prokaryotic organisms with minimal use of computer time and memory. The new system, MUMmer 2, runs three times faster while using one-third as much memory as the original MUMmer system. It has been used successfully to align the entire human and mouse genomes to
Oxford University Press.