Faster Algorithms for Sampling and Counting Biological Sequences

The identification of sequence (amino acids or nucleotides) motifs in a particular order in biological sequences has proved to be of interest. This paper describes a computing server,SSMBS, which can locate and display the occurrences of user-defined biologically important sequence motifs (a maximum of five) present in a specific order in protein and nucleotide sequences. While the server can efficiently locate motifs specified using regular expressions, it can also find occurrences of long and complex motifs. The computation is carried out by an algorithm developed using the concepts of quantifiers in regular expressions. The web server is available to users around the clock at http://dicsoft1.physics.iisc.ernet.in/ssmbs/.

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Volatilities of codons and its application in similarity analysis of biological sequences

Journal of Mathematical Chemistry ◽

10.1007/s10910-007-9235-9 ◽

2007 ◽

Vol 43 (2) ◽

pp. 864-873 ◽

Cited By ~ 3

Author(s):

Yi Zhang ◽

Jun Wang

Keyword(s):

Similarity Analysis ◽

Biological Sequences

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Compressing Similar Biological Sequences Using FM-Index

2014 Data Compression Conference ◽

10.1109/dcc.2014.47 ◽

2014 ◽

Cited By ~ 5

Author(s):

Petr Prochazka ◽

Jan Holub

Keyword(s):

Biological Sequences

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A data mining approach based on machine learning techniques to classify biological sequences

Knowledge-Based Systems ◽

10.1016/s0950-7051(01)00143-5 ◽

2002 ◽

Vol 15 (4) ◽

pp. 217-223 ◽

Cited By ~ 15

Author(s):

M. Maddouri ◽

M. Elloumi

Keyword(s):

Machine Learning ◽

Data Mining ◽

Machine Learning Techniques ◽

Biological Sequences ◽

Data Mining Approach ◽

Learning Techniques

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A singular value decomposition approach for improved taxonomic classification of biological sequences

BMC Genomics ◽

10.1186/1471-2164-12-s4-s11 ◽

2011 ◽

Vol 12 (Suppl 4) ◽

pp. S11 ◽

Cited By ~ 2

Author(s):

Anderson R Santos ◽

Marcos A Santos ◽

Jan Baumbach ◽

John A McCulloch ◽

Guilherme C Oliveira ◽

...

Keyword(s):

Singular Value Decomposition ◽

Singular Value ◽

Taxonomic Classification ◽

Biological Sequences ◽

Decomposition Approach ◽

Value Decomposition

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Association rule based frequent pattern mining in biological sequences

2013 IEEE International Conference on Computational Intelligence and Computing Research ◽

10.1109/iccic.2013.6724203 ◽

2013 ◽

Cited By ~ 1

Author(s):

A Salim ◽

S. S. Vinod Chandra

Keyword(s):

Association Rule ◽

Pattern Mining ◽

Frequent Pattern Mining ◽

Frequent Pattern ◽

Biological Sequences ◽

Rule Based

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Semiotic thoughts on biological sequence representations

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207324666210705112232 ◽

2021 ◽

Vol 24 ◽

Author(s):

Guillermo Restrepo

Keyword(s):

Research Area ◽

Biological Sequences ◽

Biological Sequence ◽

Mathematical Chemistry ◽

Dna And Rna

: The deluge of biological sequences ranging from those of proteins, DNA and RNA to genomes has increased the models for their representation, which are further used to contrast those sequences. Here we present a brief bibliometric description of the research area devoted to representation of biological sequences and highlight the semiotic reaches of this process. Finally, we argue that this research area needs further research according to the evolution of mathematical chemistry and its drawbacks are required to be overcome.

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