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DETECTING PATTERNS IN PROTEIN SEQUENCES

JOURNAL OF MOLECULAR BIOLOGY 1994年第5期239卷 698-712页

作者： NEUWALD, AF GREEN, P WASHINGTON UNIV SCH MED DEPT GENET ST LOUIS MO 63110 USA

The detection of conserved sequence patterns (motifs) in related proteins often yields valuable structural and functional insights. We describe a method that utilizes rigorous statistics and a depth-first search procedure to efficiently and exhaustively search a set of proteins for significant patterns up to a specified length. Additional procedures classify related patterns into groups and identify protein segments most likely to share a common motif. The utility of the method was demonstrated on several difficult test problems; detection of motifs among 56 protein in the acyltransferase family, detection of a dinucleotide-binding fold present within a small subset of a set of 91 distantly related and unrelated proteins, detection of the helix-turn-helix motif in 15 distantly related proteins and detection of subtle internal repeats in a prenyltransferase. In a search of a large set of sequences for internal repeats, the method detected novel ankyrin-like repeats in an Escherichia coli protein.

关键词： PATTERN RECOGNITION STATISTICAL SIGNIFICANCE alignment algorithms SEQUENCE COMPARISON AMINO ACID SEQUENCE

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Hardware acceleration of the novel two dimensional Burrows-Wheeler Aligner algorithm with maximal exact matches seed extension kernel

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IET CIRCUITS DEVICES & SYSTEMS 2021年第2期15卷 94-103页

作者： Taheri, Mahdi Ansari, Mohammad Saeed Magierowski, Sebastian Mahani, Ali Shahid Bahonar Univ Kerman Dept Elect Engn Reliable & Smart Syst Lab RSS Kerman Iran Eideticom Computat Storage Calgary AB Canada York Univ Lassonde Sch Engn Dept Elect Engn & Comp Sci Toronto ON Canada

Next-generation sequencing techniques have dramatically increased the amount of genomic data being sequenced, which calls for the acceleration of the alignment algorithms. This article proposes an FPGA-based accelerated implementation of the seed extension kernel of the Burrows-Wheeler alignment genomic mapping algorithm. The well-known Smith-Waterman algorithm is used during the seed extension to find the optimum alignment between the sequences. The state-of-the-art architectures in the literature use one-dimensional (1-D) systolic arrays to fill a similarity matrix, based on the best score out of all match combinations, mismatches and gaps are computed. The cells on the same anti-diagonal are computed in parallel in these architectures. We propose a novel 2-dimensional architecture in which all the cells on the same rows and the same columns are computed in parallel and, thereby, significantly accelerated the process. The similarity matrix cells are computed in two phases: (1) the calculation phase and (2) error compensation phase. The calculation phase roughly approximate the cell values and the approximation error is fixed up during the error compensation phase. Our simulation results show that the proposed architecture can be up to 718x and 1.7x faster than the software execution and the 1-D systolic arrays, respectively.

关键词： Burrows-Wheeler alignment genomic mapping algorithm match combinations two dimensional Burrows-Wheeler Aligner algorithm FPGA-based accelerated implementation similarity matrix cells systolic arrays 1D systolic arrays similarity matrix cell values hardware accelerators approximation error optimum alignment one-dimensional systolic arrays next-generation sequencing techniques genomic data error compensation phase hardware acceleration approximation theory calculation phase matrix algebra field programmable gate arrays Smith-Waterman algorithm alignment algorithms maximal exact matches seed extension kernel error compensation 2-dimensional architecture accelerated implementation

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AMINO-ACID SUBSTITUTION MATRICES FROM PROTEIN BLOCKS

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 1992年第22期89卷 10915-10919页

作者： HENIKOFF, S HENIKOFF, JG Howard Hughes Medical Institute Fred Hutchinson Cancer Research Center Seattle WA 98104.

Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.

关键词： AMINO ACID SEQUENCE alignment algorithms DATA BASE SEARCHING

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Protein threading by recursive dynamic programming

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JOURNAL OF MOLECULAR BIOLOGY 1999年第3期290卷 757-779页

作者： Thiele, R Zimmer, R Lengauer, T German Natl Res Ctr Informat Technol GMD Inst Algorithms & Sci Comp SCAI D-53754 St Augustin Germany

We present the recursive dynamic programming (RDP) method for the threading approach to three-dimensional protein structure prediction. RDP is based on the divide-and-conquer paradigm and maps the protein sequence whose backbone structure is to be found (the protein target) onto the known backbone structure of a model protein (the protein template) in a stepwise fashion, a technique that is similar to computing local alignments but utilising different cost functions. We begin by mapping parts of the target onto the template that show statistically significant similarity with the template sequence. After mapping, the template structure is modified in order to account for the mapped target residues. Then significant similarities between the yet unmapped parts of the target and the modified template are searched, and the resulting segments of the target are mapped onto the template. This recursive process of identifying segments in the target to be mapped onto the template and modifying the template is continued until no significant similarities between the remaining parts of target and template are found. Those parts which are left unmapped by the procedure are interpreted as gaps. The RDP method is robust in the sense that different local alignment methods can be used, several alternatives of mapping parts of the target onto the template can be handled and compared in the process, and the cost functions can be dynamically adapted to biological needs. Our computer experiments show that the RDP procedure is efficient and effective. We can thread a typical protein sequence against a database of 887 template domains in about 12 hours even on a low-cost workstation (SUN Ultra 5). in statistical evaluations on databases of known protein structures, RDP significantly outperforms competing methods. RDP has been especially valuable in providing accurate alignments for modeling active sites of proteins. RDP is part of the ToPLign system (GMD Toolbox for protein alignment) and

关键词： protein structure prediction threading alignment algorithms fold recognition alignment quality assessment

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AMINO-ACID SUBSTITUTION MATRICES FROM AN INFORMATION THEORETIC PERSPECTIVE

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JOURNAL OF MOLECULAR BIOLOGY 1991年第3期219卷 555-565页

作者： ALTSCHUL, SF National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda MD 20894.

Protein sequence alignments have become an important tool for molecular biologists. Local alignments are frequently constructed with the aid of a "substitution score matrix" that specifies a score for aligning each pair of amino acid residues. Over the years, many different substitution matrices have been proposed, based on a wide variety of rationales. Statistical results, however, demonstrate that any such matrix is implicitly a "log-odds" matrix, with a specific target distribution for aligned pairs of amino acid residues. In the light of information theory, it is possible to express the scores of a substitution matrix in bits and to see that different matrices are better adapted to different purposes. The most widely used matrix for protein sequence comparison has been the PAM-250 matrix. It is argued that for database searches the PAM-120 matrix generally is more appropriate, while for comparing two specific proteins with suspected homology the PAM-200 matrix is indicated. Examples discussed include the lipocalins, human alpha 1 B-glycoprotein, the cystic fibrosis transmembrane conductance regulator and the globins.

关键词： HOMOLOGY SEQUENCE COMPARISON STATISTICAL SIGNIFICANCE alignment algorithms PATTERN RECOGNITION

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Implementing pairwise alignments in bioinformatics with computer algebra

Implementing pairwise alignments in bioinformatics with comp...

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IEEE SoutheastCon 2006

作者： Rambally, Gerard Rambally, Rodney Prairie View A&M Univ Dept Comp Sci Prairie View TX 77446 USA Univ Trinidad & Tobago Dept Info Tech Com Arima Trinidad Tobago

ISBN: (纸本)1424401682

Newcomers to the field of bioinformatics are faced with a bewildering array of databases and tools, which use a variety of interfaces and data formats. This observation notwithstanding, an increasing number of universities now offer bioinformatics courses and majors. This paper provides a simple and inexpensive alternative to these complex databases and tools for teaching an introductory course in bioinformatics. It describes how the computer algebra package, Maple, can be used in an introductory bioinformatics course, to illustrate the concepts and methods by which alignments between two related nucleotide or polypeptide sequences can be found and evaluated. Emphasis is placed on visualizing the alignments using two and three-dimensional graphics.

关键词： alignment algorithms Dot plots Maple Pairwise alignments Sequence alignments Visualization

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Detection and classification of cardiac murmurs using segmentation techniques and artificial neural networks

Detection and classification of cardiac murmurs using segmen...

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IEEE Symposium on Computational Intelligence and Data Mining

作者： Strunic, S. L. Rios-Gutierrez, F. Alba-Flores, R. Nordehn, G. Burns, S. Univ Minnesota 1023 Univ Dr Duluth MN 55812 USA

ISBN: (纸本)9781424407057

In this paper we present the implementation of a diagnostic system based on Artificial Neural Networks (ANN) that can be used in the detection and classification of heart murmurs. Segmentation and alignment algorithms serve as important pre-processing steps before heart sounds are applied to the ANN structure. The system enables users to create a classifier that can be trained to detect virtually any desired target set of heart sounds. The output of the system is the classification of the sound as either normal or a type of heart murmur. The ultimate goal of this research is to implement a heart sounds diagnostic system that can be used to help physicians in the auscultation of patients and to reduce the number of unnecessary echocardiograms-- those that are ordered for healthy patients. Testing has been conducted using both simulated and recorded patient heart sounds as input. Three sets of results for the tested system are included herein, corresponding to three different target sets of simulated heart sounds. The system is able to classify with up to 85 +/- 7.4% accuracy and 95 +/- 6.8% sensitivity. For each target set, the accuracy rate of the ANN system is compared to the accuracy rate of a group of 2(nd) year medical students who were asked to classify heart sounds from the same group of heart sounds classified by the ANN system. System test results are also explored using recorded patient heart sounds.

关键词： acoustic signal detection diseases echocardiography medical diagnostic computing neural nets patient care patient diagnosis signal classification alignment algorithms artificial neural networks cardiac murmur classification cardiac murmur detection diagn Heart Sounds medical diagnostic computing acoustic signal detection Heart Murmurs patient diagnosis signal classification Neural network accuracy rate Echocardiography Patient Care diagnostic system maladjustment

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Character N-grams translation in cross-language information retrieval

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12th International Conference on Applications of Natural Language to Information Systems

作者： Vilares, Jesus Oakes, Michael P. Vilares, Manuel Univ A Coruna Dept Comp Sci Campus Elvinas S-N La Coruna 15071 Spain Univ Sunderland Sch Comp &Technol Sunderland SR6 0DD Durham England Univ Vigo Dept Comp Sci Orense 32004 Spain

ISBN: (纸本)9783540733508

This paper describes a new technique for the direct translation of character n-grams for use in Cross-Language Information Retrieval systems. This solution avoids the need for word normalization during indexing or translation, and it can also deal with out-of-vocabulary words. This knowledge-light approach does not rely on language-specific processing, and it can be used with languages of very different natures even when linguistic information and resources are scarce or unavailable. Our proposal also tries to achieve a higher speed during the n-gram alignment process with respect to previous approaches.

关键词： Cross-Language Information Retrieval character N-grams translation algorithms alignment algorithms association measures

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Protein structure alignment: Is there room for improvement?

Protein structure alignment: Is there room for improvement?

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International Conference on Complex, Intelligent and Software Intensive Systems

作者： Mauricio Arriagada Aleksandar Poleksic Department of Computer Science University of Tarapaca Department of Computer Science University of Northern Iowa

ISBN: (纸本)9781467312332

Recent years have seen rapid development of methods for approximate and optimal solutions to the protein structure alignment problem. Albeit slow, these methods can be extremely useful in assessing the accuracy of more efficient, heuristic algorithms. We utilize a recently developed approximation algorithm for protein structure matching to demonstrate that a deep search of the protein superposition space leads to increased alignment accuracy with respect to many well established measures of alignment quality. The results of our study suggest that a large and important part of the protein superposition space remains unexplored by current techniques for protein structure alignment.

关键词： Protein structure Structure comparison Structural alignment alignment algorithms Protein Structure alignment accuracy alignment Approximation algorithms optimal solution

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A visualization approach to Motif discovery in DNA sequences

A visualization approach to Motif discovery in DNA sequences

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IEEE SoutheastCon 2007

作者： Rambally, Gerard Prairie View A&M Univ Dept Comp Sci Prairie View TX 77446 USA

ISBN: (纸本)9781424410286

Given a set of DNA sequences, the Motif finding problem involves finding short DNA sequences or consensus patterns that occur surprisingly often, without any prior knowledge of what these patterns looks like. This paper proposes a visualization technique and algorithm for finding motifs in DNA sequences. We demonstrate that the performance of the motif finding algorithm is significantly improved with the proposed visualization technique. In the proposed method each nucleotide base {A, T C, G} in a DNA sequence is assigned a unique integer as a function of its immediate subsequent base, allowing the DNA sequence to be mapped to a corresponding numeric sequence. This numeric sequence is then plotted in 3-D space. After plotting multiple DNA sequences in the same 3-D space, approximately identical regions of the plots. are aligned by translation and rotational transformations. The images of the approximately identical regions appear as clusters in the combined sequence image and are then used to generate the l-mers alignment matrix from which the nucleotide profile matrix is computed Finally, the profile matrix is used to generate the consensus string pattern or motif.

关键词： alignment algorithms Bioinformatics Data visualization DNA sequence Motif discovery Sequence alignments

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