Smith Waterman
Mostrando 1-12 de 12 artigos, teses e dissertações.
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1. SHARED-GM: Arquitetura de Memoria Distribuıda para o Ambiente D-GM. / SHARED-GM: DISTRIBUTED MEMORY ARCHITECTURE FOR D-GM ENVIRO
O recente avanco das tecnologias de computadores impulsionaram o uso de clusters de computadores para execuc ao de aplicac oes que exijam um grande esforco computacional, tornando esta pratica uma forte tendencia atual. Acompanhando esta tendencia, o Ambiente D-GM (Distributed-Geometric Machine) constitui-se em uma ferramenta compreendendo dois modulos de so
IBICT - Instituto Brasileiro de Informação em Ciência e Tecnologia. Publicado em: 11/09/2010
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2. AnÃlise in silico de novos potenciais polimorfismos genÃticos de risco na DoenÃa de Alzheimer em bancos de dados de Microarrays
Genomic and Proteomic studies of neurodegenerative disorders require complementary approaches to integrate the massive amount of data generated in high throughput experimental procedures. We propose a Bioinformatics pipeline in which expression studies guide the selection of candidate genes that should be screened for potential new genetic variations from a
Publicado em: 2009
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3. FPGA architectures for biological sequence comparison in linear space / Arquiteturas em FPGA para comparação de sequências em espaço linear
The alignment of biological sequences is one of the more basic operations in bioinformatics. Its purpose is to find the similarity between sequences. The solution to this problem generally involves sequence comparison through dynamic programming. This kind of comparison yields optimal results but has quadratic time complexity thus justifying its hardware acc
Publicado em: 2008
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4. Desenvolvimento de hardware reconfigurável dedicado para suporte ao alinhamento de seqüencias
Encontrar e visualizar semelhanças entre seqüências de DNA permite aprofundar o conhecimento sobre genomas de organismos em Biologia Molecular. Com o número de seqüências disponíveis para consulta em alguns bancos de dados crescendo exponencialmente, surge um desafio para a ciência da computação. É o de construir sistemas de informática com desem
Publicado em: 2007
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5. Comparação Paralela Exata de Seqüências Biológicas Longas com Uso Limitado de Memória
O alinhamento de seqüências biológicas é um método muito importante usado pela biologia computacional para relacionar organismos e compreender os processos evolutivos envolvidos entre eles. O algoritmo de Smith-Waterman, método exato para obtenção de alinhamentos locais ótimos entre seqüências de DNA (ácido desoxirribonucleico), possui complexida
Publicado em: 2006
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6. Phase transitions in sequence matches and nucleic acid structure.
Analyses of phase transitions in biopolymers have previously been restricted to studies of average behavior along macromolecules. Extremal properties, such as longest helical region, can now be studied with a new family of probability distributions [Arratia, R., Gordon, L. & Waterman, M. S. (1986) Ann. Stat. 14, 971-993]. Not only is such extremal behavior a
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7. ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches
There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel processing capabilities in the form of the single instruction, multiple data (SIMD) technology are now available in common microprocessors and enable a single microprocessor to
Oxford University Press.
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8. The Genome Sequence DataBase
The Genome Sequence DataBase (GSDB) is a database of publicly available nucleotide sequences and their associated biological and bibliographic information. Several notable changes have occurred in the past year: GSDB stopped accepting data submissions from researchers; ownership of data submitted to GSDB was transferred to GenBank; sequence analysis capabili
Oxford University Press.
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9. Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters
The CluSTr database (http://www.ebi.ac.uk/clustr/) offers an automatic classification of SWISS-PROT+TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pair-wise sequence comparisons between proteins using the Smith–Waterman algorithm. The analysis, carried out on different levels of protein similarity, yields a hier
Oxford University Press.
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10. Computer methods for locating kinetoplastid cryptogenes.
RNA editing in the mitochondria of kinetoplastid protoza involves the insertion and/or deletion of precise numbers of uridine residues at precise locations in the numbers of uridine residues at precise locations in the transcribed RNA of certain genes. These genes are known as cryptogenes. In this paper we study computational algorithms to search for unknown
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11. BALSA: Bayesian algorithm for local sequence alignment
The Smith–Waterman algorithm yields a single alignment, which, albeit optimal, can be strongly affected by the choice of the scoring matrix and the gap penalties. Additionally, the scores obtained are dependent upon the lengths of the aligned sequences, requiring a post-analysis conversion. To overcome some of these shortcomings, we developed a Bayesian al
Oxford University Press.
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12. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
Pairwise sequence comparison methods have been assessed using proteins whose relationships are known reliably from their structures and functions, as described in the scop database [Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia C. (1995) J. Mol. Biol. 247, 536–540]. The evaluation tested the programs blast [Altschul, S. F., Gish, W., Miller, W., Mye
The National Academy of Sciences.