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380
A greedy algorithm for aligning DNA sequences
 J. COMPUT. BIOL
, 2000
"... For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy a ..."
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Cited by 240 (15 self)
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For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy alignment algorithm with particularly good performance and show that it computes the same alignment as does a certain dynamic programming algorithm, while executing over 10 times faster on appropriate data. An implementation of this algorithm is currently used in a program that assembles the UniGene database at the National Center for Biotechnology Information.
Optimal alignments in linear space
 CABIOS
, 1988
"... Space, not time, is often the limiting factor when computing optimal sequence alignments, and a number of recent papers in the biology literature have proposed spacesaving strategies. However, a 1975 computer science paper by Hirschberg presented a method that is superior to the newer proposals, bo ..."
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Cited by 181 (3 self)
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Space, not time, is often the limiting factor when computing optimal sequence alignments, and a number of recent papers in the biology literature have proposed spacesaving strategies. However, a 1975 computer science paper by Hirschberg presented a method that is superior to the newer proposals, both in theory and in practice. The goal of this note is to give Hirschberg’s idea the visibility it deserves by developing a linearspace version of Gotoh’s algorithm, which accommodates affine gap penalties. A portable Csoftware package implementing this algorithm is available on the BIONET free of charge.
PROBCONS: Probabilistic consistencybased multiple sequence alignment
 Genome Res
, 2005
"... To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however, is a difficult computational problem because of not only the high computational cost but also the lack of proper objec ..."
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Cited by 142 (7 self)
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To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however, is a difficult computational problem because of not only the high computational cost but also the lack of proper objective functions for measuring alignment quality. In this paper, we introduce probabilistic consistency, a novel scoring function for multiple sequence comparisons. We present PROBCONS, a practical tool for progressive protein multiple sequence alignment based on probabilistic consistency, and evaluate its performance on several standard alignment benchmark datasets. On the BAliBASE, SABmark, and PREFAB benchmark alignment databases, PROBCONS achieves statistically significant improvement over other leading methods while maintaining practical speed. PROBCONS is publicly available as a web resource. Source code and executables are available under the GNU Public License at
Twister: A runtime for iterative MapReduce
 In The First International Workshop on MapReduce and its Applications
, 2010
"... MapReduce programming model has simplified the implementation of many data parallel applications. The simplicity of the programming model and the quality of services provided by many implementations of MapReduce attract a lot of enthusiasm among distributed computing communities. From the years of e ..."
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Cited by 94 (8 self)
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MapReduce programming model has simplified the implementation of many data parallel applications. The simplicity of the programming model and the quality of services provided by many implementations of MapReduce attract a lot of enthusiasm among distributed computing communities. From the years of experience in applying MapReduce to various scientific applications we identified a set of extensions to the programming model and improvements to its architecture that will expand the applicability of MapReduce to more classes of applications. In this paper, we present the programming model and the architecture of Twister an enhanced MapReduce runtime that supports iterative MapReduce computations efficiently. We also show performance comparisons of Twister with other similar runtimes such as Hadoop and DryadLINQ for large scale data parallel applications.
A New Algorithm for the Alignment of Phonetic Sequences
, 2000
"... Alignment of phonetic sequences is a necessary step in many applications in computational phonology. After discussing various approaches to phonetic alignment, I present a new algorithm that combines a number of techniques developed for sequence comparison with a scoring scheme for computing phoneti ..."
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Cited by 48 (10 self)
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Alignment of phonetic sequences is a necessary step in many applications in computational phonology. After discussing various approaches to phonetic alignment, I present a new algorithm that combines a number of techniques developed for sequence comparison with a scoring scheme for computing phonetic similarity on the basis of multivalued features. The algorithm performs better on cognate alignment, in terms of accuracy and efficiency, than other algorithms reported in the literature.
Fast evaluation of internal loops in RNA secondary structure prediction
, 1999
"... Motivation: Though not as abundant in known biological processes as proteins, RNA molecules serve as more than mere intermediaries between DNA and proteins. Research in the last 15 years demonstrates that RNA molecules serve in many roles, including catalysis. Furthermore, RNA secondary structure pr ..."
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Cited by 46 (3 self)
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Motivation: Though not as abundant in known biological processes as proteins, RNA molecules serve as more than mere intermediaries between DNA and proteins. Research in the last 15 years demonstrates that RNA molecules serve in many roles, including catalysis. Furthermore, RNA secondary structure prediction based on free energy rules for stacking and loop formation remains one of the few major breakthroughs in the eld of structure prediction, as minimum free energy structures and related quantities can be computed with full mathematical rigor. However, with the current energy parameters, the algorithms used hitherto suer the disadvantage of either employing heuristics that risk (though highly unlikely) missing the optimal structure or becoming prohibitively timeconsuming for moderate to large sequences. Results: We present a new method to evaluate internal loops utilizing currently used energy rules. This method reduces the time complexity of this part of the structure prediction f...
Alignmentfree sequence comparisona review
 Bioinformatics
, 2003
"... Motivation: Genetic recombination and, in particular, genetic shuffling are at odds with sequence comparison by alignment, which assumes conservation of contiguity between homologous segments. A variety of theoretical foundations are being used to derive alignmentfree methods that overcome this lim ..."
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Cited by 42 (5 self)
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Motivation: Genetic recombination and, in particular, genetic shuffling are at odds with sequence comparison by alignment, which assumes conservation of contiguity between homologous segments. A variety of theoretical foundations are being used to derive alignmentfree methods that overcome this limitation. The formulation of alternative metrics for dissimilarity between sequences and their algorithmic implementations are reviewed. Results: The overwhelming majority of work on alignmentfree sequence has taken place in the past two decades, with most reports published in the past 5 years. Two main categories of methods have been proposed—methods based on word (oligomer) frequency, and methods that do not require resolving the sequence with fixed word length segments. The first category is based on the statistics of word frequency, on the distances defined in a Cartesian space defined by the frequency vectors, and on the information content of frequency distribution. The second category includes the use of Kolmogorov complexity and Chaos Theory. Despite their low visibility, alignmentfree metrics are in fact already widely used as preselection filters for alignmentbased querying of large applications. Recent work is furthering their usage as a scaleindependent methodology that is capable of recognizing homology when loss of contiguity is beyond the possibility of alignment. Availability: Most of the alignmentfree algorithms reviewed were implemented in MATLAB code and are available
Scoring Hidden Markov Models
"... Motivation: Statistical sequence comparison techniques, such as hidden Markov models and generalized pro les, calculate the probability that a sequence was generated by a given model. Logodds scoring is a means of evaluating this probability by comparing it to a null hypothesis, usually a simpler s ..."
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Cited by 37 (5 self)
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Motivation: Statistical sequence comparison techniques, such as hidden Markov models and generalized pro les, calculate the probability that a sequence was generated by a given model. Logodds scoring is a means of evaluating this probability by comparing it to a null hypothesis, usually a simpler statistical model intended to represent the universe of sequences as a whole, rather than the group of interest. Such scoring leads to two immediate questions: what should the null model be, and what threshold of logodds score should be deemed a match to the model. Results: This paper experimentally analyses these two issues. Within the context of the Sequence Alignment and Modeling software suite (SAM), we consider a variety ofnull models and suitable thresholds. Additionally, we consider HMMer's logodds scoring and SAM's original Zscoring method. Among the null model choices, a simple looping null model that emits characters according to the geometric mean of the character probabilities in the columns modeled by the HMM performs well or best across all four discrimination experiments.
Accurate formula for pvalues of gapped local sequence and profile alignments
 J. Mol. Biol
, 2000
"... A simple general approximation for the distribution of gapped local alignment scores is presented, suitable for assessing significance of comparisons between two protein sequences or a sequence and a profile. The approximation takes account of the scoring scheme (ie gap penalty and substitution matr ..."
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Cited by 37 (1 self)
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A simple general approximation for the distribution of gapped local alignment scores is presented, suitable for assessing significance of comparisons between two protein sequences or a sequence and a profile. The approximation takes account of the scoring scheme (ie gap penalty and substitution matrix or profile), sequence composition and length. Use of this formula means it is unnecessary to fit an extremevalue distribution to simulations or to the results of databank searches. The method is based on the theoretical ideas introduced in (Mott & Tribe, 1999). Extensive simulation studies show that scorethresholds produced by the method are accurate to within ±5 % 95 % of the time. We also investigate factors which affect the accuracy of alignment statistics, and show that any method based on asymptotic theory is limited because asymptotic behaviour is not strictly achieved for many real protein sequences, due to extreme composition effects. Consequently it may not be practicable to find a general formula that is significantly more accurate until the subasymptotic behaviour of alignments is better understood.
Sequence Comparison Significance and Poisson Approximation
 Stat. Sci
, 1994
"... The ChenStein method of Poisson approximation has been used to establish theorems about comparison of two DNA or protein sequences. The most useful result for sequence alignment applies to alignment scoring for aligned letters and no gaps. However there has not been a valid method to assign statist ..."
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Cited by 36 (4 self)
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The ChenStein method of Poisson approximation has been used to establish theorems about comparison of two DNA or protein sequences. The most useful result for sequence alignment applies to alignment scoring for aligned letters and no gaps. However there has not been a valid method to assign statistical significance to alignment scores with gaps. In this paper we extend Poisson approximation techniques using the Aldous clumping heuristic to a practical method of estimating statistical significance.