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Journal Article
Algorithms for Molecular Biology, ISSN 1748-7188, 12/2017, Volume 12, Issue 1, pp. 27 - 12
Background: Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between pairs of input sequences.... 
Phylogeny | Alignment-free | Kmacs | Pattern matching | Average common substring | TREES | GENOMES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DISTANCES | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Nucleotide sequencing | Analysis | DNA | DNA sequencing
Journal Article
Theoretical Computer Science, ISSN 0304-3975, 10/2017, Volume 698, pp. 100 - 112
Phylogeny inference has moved in recent years from the analysis of a single or few proteins to that of whole proteomes. However, the reconstruction of... 
Mismatches | Alignment free distances | Distributed systems | Bioinformatics | Average common substring | RECONSTRUCTION | PROKARYOTIC PHYLOGENY | HADOOP | SEQUENCE ALIGNMENT | COMPUTER SCIENCE, THEORY & METHODS | SCALE | COMMON SUBSTRING APPROACH | GENOME TREES | Proteins | Analysis | Algorithms
Journal Article
Journal of Complexity, ISSN 0885-064X, 02/2013, Volume 29, Issue 1, pp. 44 - 52
In this paper, we generalize the inclusion constrained longest common subsequence (CLCS) problem to the hybrid CLCS problem which is the combination of the... 
Sequential substring | Algorithm design | Constrained LCS | Bioinformatics | Longest common subsequence | LCS PROBLEM | MATHEMATICS, APPLIED | COMPUTER SCIENCE, THEORY & METHODS | Algorithms
Journal Article
BIOINFORMATICS, ISSN 1367-4803, 06/2019, Volume 35, Issue 11, pp. 1820 - 1828
Motivation: Sequence analysis is arguably a foundation of modern biology. Classic approaches to sequence analysis are based on sequence alignment, which is... 
COMMON SUBSTRING APPROACH | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY
Journal Article
Genomics, ISSN 0888-7543, 12/2019, Volume 111, Issue 6, pp. 1574 - 1582
Given the vast amount of genomic data, alignment-free sequence comparison methods are required due to their low computational complexity. k-mer based methods... 
ALIGNMENT | COMMON SUBSTRING APPROACH | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY
Journal Article
The Protein Journal, ISSN 1572-3887, 3/2011, Volume 30, Issue 3, pp. 167 - 172
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 07/2014, Volume 42, Issue 1, pp. W7 - W11
In this article, we present a user-friendly web interface for two alignment-free sequence-comparison methods that we recently developed. Most alignment-free... 
PHYLOGENY | COMMON SUBSTRING APPROACH | GENOMES | SEARCH | RECONSTRUCTION | BIOCHEMISTRY & MOLECULAR BIOLOGY | Sequence Analysis, Protein - methods | User-Computer Interface | Sequence Alignment | Algorithms | Software | Internet | Phylogeny | Sequence Analysis, DNA - methods
Journal Article
SCIENTIFIC REPORTS, ISSN 2045-2322, 03/2019, Volume 9, Issue 1, pp. 3753 - 18
A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with... 
CLASSIFICATION | DISTANCE | EVOLUTION | COMMON SUBSTRING APPROACH | MULTIDISCIPLINARY SCIENCES | Fungi | Algorithms | Next-generation sequencing | Nucleotide sequence | Arbuscular mycorrhizas | Phylogeny | Markov analysis | Deoxyribonucleic acid--DNA
Journal Article
Bioinformatics, ISSN 1367-4803, 04/2015, Volume 31, Issue 8, pp. 1169 - 1175
Journal Article
GENOME BIOLOGY, ISSN 1474-760X, 07/2019, Volume 20, Issue 1, pp. 144 - 18
Journal Article
Scientific Reports, ISSN 2045-2322, 12/2017, Volume 7, Issue 1, pp. 12226 - 11
With sharp increasing in biological sequences, the traditional sequence alignment methods become unsuitable and infeasible. It motivates a surge of fast... 
CHAOS GAME REPRESENTATION | DNA-SEQUENCES | DSDNA VIRUSES | EVOLUTION | FOURIER-TRANSFORM | PHYLOGENETIC ANALYSIS | MULTIDISCIPLINARY SCIENCES | ALIGNMENT-FREE METHOD | MODEL | COMMON SUBSTRING APPROACH | MOLECULAR PHYLOGENY | Nucleotide sequence | Macromolecules | Phylogeny
Journal Article