sequence alignment algorithms
Multiple sequence alignment algorithms for the phylogenic analysis of chloroplast DNA
... Progressive alignment methods are the most commonly used and have the advantage of speed and simplicity (Notredame ...Progressive alignment successively aligns pairs of sequences using pairwise ...
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Instability in progressive multiple sequence alignment algorithms
... real alignment scores using an amino acid weight matrix such as BLOSUM [7], the number of possible scores is still finite although much greater than with k-tuple ...such alignment scores is limited how- ...
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Analysing Multiple DNA Sequence Alignment Algorithms Smith Waterman Algorithm and Parallel Smith Waterman Algorithm
... DNA sequence alignment is one of the important research topics of ...automated sequence analysis facilitates everything from functional classification & structural determination of proteins, to ...
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A Survey of the State of the Art Parallel Multiple Sequence Alignment Algorithms on Multicore Systems
... genetic algorithms through a set of mutation and crossover operations to the expected alignment results to find the best alignment solution for a set of given ...multiple sequence ...
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A RANDOMIZED ALGORITHM FOR FAST SEQUENCE ALIGNMENT
... since sequence alignment gained significance, a large number of algorithms have been ...pairwise sequence alignment algorithms and multiple sequence alignment ...
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Multiple Many to Many Sequence Alignment for Combining String Valued Variables: A G2P Experiment
... many-to-many alignment models investigated in this work could act as a preprocess- ing step in this setup, since the alignment precisely serves the functionality of segmenting the strings into equal number ...
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Heuristics for multiobjective multiple sequence alignment
... Tables 3 and 4 report results obtained for PILS on the same benchmark sets, averaged over 10 runs, for k-block size equals to 2; we recall that we use Clust and Tcoffee as starting alignments. The results reported in the ...
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Horizontal transfer and proliferation of Tsu4 in Saccharomyces paradoxus
... complete sequence with high similarity to Tsu4 from a ...query sequence ( > 80% coverage and > 80% iden- ...one sequence from S. mikatae, one sequence from ...one sequence each ...
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Fractal MapReduce decomposition of sequence alignment
... The use of JavaScript to develop an implementation of the alignment-free [5] map-reduce decomposition of sequence analysis could be justified solely on grounds of convenience. Since web browsers are ...
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Some studies on protein structure alignment algorithms
... Mass [14], Mapsci [32], and Smolign [64], which is taken into account when the goal is to find a struc- turally conserved subset of residues among the proteins to obtain knowledge about their evolution and origin. It ...
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Effect of positional dependence and alignment strategy on modeling transcription factor binding sites
... the probability that the known negative example would score higher than the known positive example — produc- ing a false positive. PS scopes larger than a certain value do not capture any new position-pair matches, yet ...
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Algorithms for Learning Kernels Based on Centered Alignment
... two algorithms that each work in two subsequent stages (Sections ...two algorithms differ in the way centered alignment is used to learn ...centered alignment of that matrix with the target ...
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ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos
... stacked sequence representation since a curated alignment had grown to several hundred homologs ...an alignment to a matrix, color-shaded according to the residue frequency in the MSA ...avoid ...
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Sequence embedding for fast construction of guide trees for multiple sequence alignment
... worse that using the default guide trees. The bad news is that all guide trees are ineffective anyway. For the remain- ing four test cases, the randomised Clustal guide trees are clearly inferior to both the default ...
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Efficient Alignment Algorithms for DNA Sequencing Data
... The Illumina sequencing technology can be summarized in three core steps - amplify, se- quence and analyze. The process begins by breaking up a DNA sequence into smaller frag- ments. These fragments are attached ...
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Insights of Rv2921c (Ftsy) Gene of Mycobacterium tuberculosis H37Rv To Prove Its Significance by Computational Approach
... model protein is good and satisfactory. The Verify3D strategy evaluates protein structure by utilizing three-dimensional profiles. This program examines the similarity of a nuclear model (3D) with its own amino acid ...
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Conserved antigenic sites between MERS-CoV and Bat-coronavirus are revealed through sequence analysis
... marked sequence divergence in the spike protein of pipistrellus bat coronavirus HKU5 in Japanese pipistrelle: implications for the origin of the novel Middle East respiratory syndrome ...
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Optimization of sequence alignment for simple sequence repeat regions
... simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the ...
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A Design of a Hybrid System for DNA Sequence Alignment
... Each sequence will be stored into an input array of a number of positions equal to the input sequence length stored in it and each position has 2 flip flops A and ...
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Remmert, Michael (2011): Fast, sensitive protein sequence searches using iterative pairwise comparison of hidden Markov models. Dissertation, LMU München: Fakultät für Chemie und Pharmazie
... an alignment as a conditional random field (CRF) (Do et ...the sequence features as it is done in the RAPTOR servers (Peng and Xu, ...score, sequence-sequence score, profile-sequence ...
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