Circular sequence comparison: algorithms and applications. [PDF]
Algorithms Mol Biol, 2016 Sequence comparison is a fundamental step in many important tasks in bioinformatics; from phylogenetic reconstruction to the reconstruction of genomes. Traditional algorithms for measuring approximation in sequence comparison are based on the notions of distance or similarity, and are generally computed through sequence alignment techniques.
Grossi R +6 more
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Pairwise sequence comparison data of the DNA barcodes of aquatic insects [PDF]
Data in Brief, 2020 This study compared the DNA sequences of cytochrome coxidase subunit I (COI) and histone H3 of Ephemeroptera, Odonata, Plecoptera, and Trichoptera in a pairwise manner, and calculated the sequence similarities based on uncorrected P-distance (number of ...
Koji Inai, Kei Wakimura, Mikio Kato
doaj +2 more sources
A biological sequence comparison algorithm using quantum computers [PDF]
Scientific Reports, 2023 Genetic information is encoded as linear sequences of nucleotides, represented by letters ranging from thousands to billions. Differences between sequences are identified through comparative approaches like sequence analysis, where variations can occur ...
Büsra Kösoglu-Kind +5 more
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Understanding the Genetic Diversity of Picobirnavirus: A Classification Update Based on Phylogenetic and Pairwise Sequence Comparison Approaches [PDF]
Viruses, 2021 Picobirnaviruses (PBVs) are small, double stranded RNA viruses with an ability to infect a myriad of hosts and possessing a high degree of genetic diversity. PBVs are currently classified into two genogroups based upon classification of a 200 nt sequence
Lester J. Perez +2 more
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Sequence Comparison of Vaginolysin from Different Gardnerella Species [PDF]
Pathogens, 2021 Gardnerella vaginalis has recently been split into 13 distinct species. In this study, we tested the hypotheses that species-specific variations in the vaginolysin (VLY) amino acid sequence could influence the interaction between the toxin and vaginal ...
Erin M. Garcia +5 more
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Sequence Comparison in Historical Linguistics [PDF]
, 2021 The comparison of sound sequences (words, morphemes) constitutes the core of many techniques and methods in historical linguistics. With the help of these techniques, corresponding sounds can be determined, historically related words can be identified, and the history of languages can be uncovered.
List, Mattis, Mattis List
openaire +4 more sources
Benchmarking of alignment-free sequence comparison methods [PDF]
Genome Biology, 2019 Background Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their
Andrzej Zielezinski +18 more
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Alignment-free sequence comparison: benefits, applications, and tools [PDF]
Genome Biology, 2017 Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences.
Andrzej Zielezinski +3 more
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On an alternative sequence comparison statistic of Steele [PDF]
Discrete Mathematics & Theoretical Computer Science, 2020 The purpose of this paper is to study a statistic that is used to compare the similarity between two strings, which is first introduced by Michael Steele in 1982.
Ümit Işlak, Alperen Y. Özdemir
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Integrating overlapping structures and background information of words significantly improves biological sequence comparison. [PDF]
PLoS ONE, 2011 Word-based models have achieved promising results in sequence comparison. However, as the important statistical properties of words in biological sequence, how to use the overlapping structures and background information of the words to improve sequence ...
Qi Dai +5 more
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