Sequence Comparison Methods Can Be Used to Study Speech Perception

1992 ◽  
Author(s):  
Lynne E. Bernstein ◽  
Marilyn E. Demorest
Keyword(s):  
Speech Perception ◽  
Sequence Comparison ◽  
Comparison Methods

scholarly journals Benchmarking of alignment-free sequence comparison methods

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Andrzej Zielezinski ◽  
Hani Z. Girgis ◽  
Guillaume Bernard ◽  
Chris-Andre Leimeister ◽  
Kujin Tang ◽  
...  
Keyword(s):  
Sequence Comparison ◽  
Alignment Free ◽  
Comparison Methods

A survey of multiple sequence comparison methods

1992 ◽  
Vol 54 (4) ◽  
pp. 563-598 ◽  
Author(s):  
S. C. Chan ◽  
A. K. C. Wong ◽  
D. K. Y. Chiu
Keyword(s):  
Sequence Comparison ◽  
Multiple Sequence ◽  
Comparison Methods

Whole-Sequence Comparison Methods

2015 ◽  
pp. 109-152
Author(s):  
Benjamin Cornwell
Keyword(s):  
Sequence Comparison ◽  
Comparison Methods

Protein sequence comparison: methods and significance

1991 ◽  
Vol 4 (4) ◽  
pp. 375-383 ◽  
Author(s):  
Patrick Argos ◽  
Martin Vingron ◽  
Gerhard Vogt
Keyword(s):  
Protein Sequence ◽  
Sequence Comparison ◽  
Comparison Methods ◽  
Protein Sequence Comparison

scholarly journals SAINT: automatic taxonomy embedding and categorization by Siamese triplet network

2021 ◽  
Author(s):  
Yang Young Lu ◽  
Yiwen Wang ◽  
Fang Zhang ◽  
Jiaxing Bai ◽  
Ying Wang
Keyword(s):  
Sequence Analysis ◽  
Sequence Comparison ◽  
Large Scale ◽  
Sequence Data ◽  
Comparison Method ◽  
Supplementary Information ◽  
Data Alignment ◽  
Alignment Free ◽  
Comparison Methods ◽  
Real World Datasets

AbstractMotivationUnderstanding the phylogenetic relationship among organisms is the key in contemporary evolutionary study and sequence analysis is the workhorse towards this goal. Conventional approaches to sequence analysis are based on sequence alignment, which is neither scalable to large-scale datasets due to computational inefficiency nor adaptive to next-generation sequencing (NGS) data. Alignment-free approaches are typically used as computationally effective alternatives yet still suffering the high demand of memory consumption. One desirable sequence comparison method at large-scale requires succinctly-organized sequence data management, as well as prompt sequence retrieval given a never-before-seen sequence as query.ResultsIn this paper, we proposed a novel approach, referred to as SAINT, for efficient and accurate alignment-free sequence comparison. Compared to existing alignment-free sequence comparison methods, SAINT offers advantages in two aspects: (1) SAINT is a weakly-supervised learning method where the embedding function is learned automatically from the easily-acquired data; (2) SAINT utilizes the non-linear deep learning-based model which potentially better captures the complicated relationship among genome sequences. We have applied SAINT to real-world datasets to demonstrate its empirical utility, both qualitatively and quantitatively. Considering the extensive applicability of alignment-free sequence comparison methods, we expect SAINT to motivate a more extensive set of applications in sequence comparison at large scale.AvailabilityThe open source, Apache licensed, python-implemented code will be available upon acceptance.Supplementary informationSupplementary data are available at Bioinformatics online.

A NOTE ON COMPLEXITY OF GENETIC MUTATIONS

2011 ◽  
Vol 03 (03) ◽  
pp. 269-286 ◽  
Author(s):  
BHADRACHALAM CHITTURI
Keyword(s):  
Dna Sequencing ◽  
Dna Sequence ◽  
Physical Mapping ◽  
Sequence Comparison ◽  
Genetic Mutation ◽  
Genetic Mutations ◽  
Comparison Methods ◽  
Np Complete ◽  
String Models ◽  
Dna Sequence Comparison

Genes, the functional segments of DNA, can be modeled akin to DNA by quaternary strings. Pevzner and Waterman posed various problems pertaining to DNA, e.g. DNA physical mapping, DNA sequencing, and DNA sequence comparison. DNA sequence comparison methods aim to compute the genetic mutation distance. Genetic mutation, a change that happens within a gene, can be modeled by an operation like a transposition or a reversal over a string where a string models a gene. The complexity of transforming quaternary strings under a given operation is equivalent to the complexity of computing the corresponding genetic mutation distance. We show that the string transformation distance under signed prefix reversals, translocations and transreversals is NP-complete.

scholarly journals EXPLORING ALIGNMENT-FREE SEQUENCE COMPARISON METHODS TO ELUCIDATE PATTERNS OF EVOLUTION AND HETEROGENEITY IN LONGITUDINAL GLIOMA PATIENT COHORTS

2018 ◽  
Vol 20 (suppl_5) ◽  
pp. v348-v348
Author(s):  
Aideen Roddy ◽  
Anna Jurek ◽  
David Gonzalez ◽  
Manuel Salto-Tellez ◽  
Kevin Prise ◽  
...  
Keyword(s):  
Sequence Comparison ◽  
Glioma Patient ◽  
Alignment Free ◽  
Comparison Methods

scholarly journals Testing statistical significance scores of sequence comparison methods with structure similarity

2006 ◽  
Vol 7 (1) ◽  
Author(s):  
Tim Hulsen ◽  
Jacob de Vlieg ◽  
Jack AM Leunissen ◽  
Peter MA Groenen
Keyword(s):  
Sequence Comparison ◽  
Statistical Significance ◽  
Comparison Methods ◽  
Structure Similarity

scholarly journals Assessing sequence comparison methods with the average precision criterion

2003 ◽  
Vol 19 (18) ◽  
pp. 2456-2460 ◽  
Author(s):  
Z. Chen
Keyword(s):  
Sequence Comparison ◽  
Average Precision ◽  
Comparison Methods

A survey of multiple sequence comparison methods

1992 ◽  
Vol 54 (4) ◽  
pp. 563-598 ◽  
Author(s):  
S CHAN ◽  
A WONG ◽  
D CHIU
Keyword(s):  
Sequence Comparison ◽  
Multiple Sequence ◽  
Comparison Methods
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