Pairwise Alignment
Mostrando 1-12 de 59 artigos, teses e dissertações.
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1. Alinhamento de seqüências biológicas com o uso de algoritmos genéticos.
A comparação de seqüências de genomas de organismos é uma das aplicações computacionais mais utilizadas por biólogos moleculares. Esta operação serve de suporte para outros processos como, por exemplo, a determinação da estrutura tridimensional de proteínas. Durante os últimos anos, tem- se observado uma grande expansão na utilização de Algo
Publicado em: 2005
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2. BLOOM BLAST Object Oriented Management: uma solução integrada para gerenciamento dos resultados do BLAST por meio de um paradigma orientado a objetos
Considered a special subject since the beginning of the 80s, bioinformatics can be defined as a way that covers all aspects of acquisition, processing, storage, distribution, analysis and interpretation of biological information. All this happens in a narrow sinergy with the molecular biology fundamental paradigm, which postulates that the genetic informatio
Publicado em: 2003
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3. Multiple sequence alignment with hierarchical clustering.
An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers. The approach is based on the conventional dynamic-programming method of pairwise alignment. Initially, a hierarchical clustering of the sequences is performed using the matrix of the pairwise alignment
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4. A flexible multiple sequence alignment program.
The 'regions' method for multisequence alignment used in the previously reported program MALIGN has been generalized to include recursive refinement so that unaligned portions between two regions at the current level of resolution can be handled with increased resolution. Additionally, there is incorporated a limiting of the number of regions to be used at a
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5. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames.
DNA translation frames can be disrupted for several reasons, including: (i) errors in sequence determination; (ii) RNA processing, such as intron removal and guide RNA editing; (iii) less commonly, polymerase frameshifting during transcription or ribosomal frameshifting during translation. Frameshifts frequently confound computational activities involving ho
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6. An algorithm for progressive multiple alignment of sequences with insertions
Dynamic programming algorithms guarantee to find the optimal alignment between two sequences. For more than a few sequences, exact algorithms become computationally impractical, and progressive algorithms iterating pairwise alignments are widely used. These heuristic methods have a serious drawback because pairwise algorithms do not differentiate insertions
National Academy of Sciences.
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7. Contact-based sequence alignment
This paper introduces the novel method of contact-based protein sequence alignment, where structural information in the form of contact mutation probabilities is incorporated into an alignment routine using contact-mutation matrices (CAO: Contact Accepted mutatiOn). The contact-based alignment routine optimizes the score of matched contacts, which involves f
Oxford University Press.
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8. Software tools for analyzing pairwise alignments of long sequences.
Pairwise comparison of long stretches of genomic DNA sequence can identify regions conserved across species, which often indicate functional significance. However, the novel insights frequently must be windowed from a flood of information; for instance, running an alignment program on two 50-kilobase sequences might yield over a hundred pages of alignments.
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9. DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors
BioMed Central.
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10. A tool for multiple sequence alignment.
Multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence-structure relationships. Until recently, it has been impractical to apply dynamic programming, the most widely accepted method for producing pairwise alignments, to comparisons of more than three sequences. We describe the design and application of a
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11. MATRAS: a program for protein 3D structure comparison
The recent accumulation of large amounts of 3D structural data warrants a sensitive and automatic method to compare and classify these structures. We developed a web server for comparing protein 3D structures using the program Matras (http://biunit.aist-nara.ac.jp/matras). An advantage of Matras is its structure similarity score, which is defined as the log-
Oxford University Press.
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12. Molecular Identification of Enterovirus by Analyzing a Partial VP1 Genomic Region with Different Methods
VP1 is the most suitable region for use in the identification of enterovirus. Although VP1 sequencing methods may vary, it is necessary to agree on a common strategy of sequence analysis. Identification of a strain type may be achieved by three different approaches: pairwise sequence alignment, multiple-sequence alignment, and phylogenetic inference. Other m
American Society for Microbiology.