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

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

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

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 Multiple Sequence Comparison and Consistency on Multipartite Graphs

1995 ◽  
Vol 16 (1) ◽  
pp. 1-22 ◽  
Author(s):  
M. Vingron ◽  
P.A. Pevzner
Keyword(s):  
Sequence Comparison ◽  
Multiple Sequence ◽  
Multipartite Graphs

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.

[27] Multiple sequence comparison

1990 ◽  
pp. 438-447 ◽  
Author(s):  
David J. Bacon ◽  
Wayne F. Anderson
Keyword(s):  
Sequence Comparison ◽  
Multiple Sequence

A multiple sequence comparison method

1993 ◽  
Vol 55 (2) ◽  
pp. 465-486 ◽  
Author(s):  
A WONG ◽  
S CHAN ◽  
D CHIU
Keyword(s):  
Sequence Comparison ◽  
Comparison Method ◽  
Multiple Sequence
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