Approximate Pattern Matching for DNA Sequence Data

Storing and processing of large DNA sequences has always been a major problem due to increasing volume of DNA sequence data. However, a number of solutions have been proposed but they require significant computation and memory. Therefore, an efficient storage and pattern matching solution is required for DNA sequencing data. Bloom filters (BFs) represent an efficient data structure, which is mostly used in the domain of bioinformatics for classification of DNA sequences. In this paper, we explore more dimensions where BFs can be used other than classification. A proposed solution is based on Multiple Bloom Filters (MBFs) that finds all the locations and number of repetitions of the specified pattern inside a DNA sequence. Both of these factors are extremely important in determining the type and intensity of any disease. This paper serves as a first effort towards optimizing the search for location and frequency of substrings in DNA sequences using MBFs. We expect that further optimizations in the proposed solution can bring remarkable results as this paper presents a proof of concept implementation for a given set of data using proposed MBFs technique. Performance evaluation shows improved accuracy and time efficiency of the proposed approach.

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Using DNA sequence data to investigate the invasive spotted lanternfly's origin, parasitoids, and microbial associates

10.1603/ice.2016.109017 ◽

2016 ◽

Author(s):

Julie M. Urban

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Dna Sequence Data

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DNA sonification for public engagement in bioinformatics

BMC Research Notes ◽

10.1186/s13104-021-05685-7 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Heleen Plaisier ◽

Thomas R. Meagher ◽

Daniel Barker

Keyword(s):

Dna Sequence ◽

Public Engagement ◽

Sequence Data ◽

Sensory Perception ◽

Data Representation ◽

Sequence Information ◽

Dna Sequence Data ◽

Public Events ◽

Dna Base ◽

Alternative Means

Abstract Objective Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification. Results We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education.

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When DNA sequence data and morphological results fit together: Phylogenetic position of Crenubiotus within Macrobiotoidea (Eutardigrada) with description of Crenubiotus ruhesteini sp. nov

Journal of Zoological Systematics & Evolutionary Research ◽

10.1111/jzs.12449 ◽

2021 ◽

Author(s):

Roberto Guidetti ◽

Ralph O. Schill ◽

Ilaria Giovannini ◽

Edoardo Massa ◽

Sara Elena Goldoni ◽

...

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Phylogenetic Position ◽

Dna Sequence Data

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A new Liopeltis Fitzinger, 1843 (Squamata: Colubridae) from Pulau Tioman, Peninsular Malaysia

Zootaxa ◽

10.11646/zootaxa.4766.3.6 ◽

2020 ◽

Vol 4766 (3) ◽

pp. 472-484

Author(s):

HANNAH E. SOM ◽

L. LEE GRISMER ◽

PERRY L. JR. WOOD ◽

EVAN S. H. QUAH ◽

RAFE M. BROWN ◽

...

Keyword(s):

Mitochondrial Dna ◽

New Species ◽

Dna Sequence ◽

Rare Species ◽

Sequence Data ◽

Peninsular Malaysia ◽

Tropical Asia ◽

Dna Sequence Data ◽

A New Species ◽

Lines Of Evidence

Liopeltis is a genus of poorly known, infrequently sampled species of colubrid snakes in tropical Asia. We collected a specimen of Liopeltis from Pulau Tioman, Peninsular Malaysia, that superficially resembled L. philippina, a rare species that is endemic to the Palawan Pleistocene Aggregate Island Complex, western Philippines. We analyzed morphological and mitochondrial DNA sequence data from the Pulau Tioman specimen and found distinct differences to L. philippina and all other congeners. On the basis of these corroborated lines of evidence, the Pulau Tioman specimen is described as a new species, L. tiomanica sp. nov. The new species occurs in sympatry with L. tricolor on Pulau Tioman, and our description of L. tiomanica sp. nov. brings the number of endemic amphibians and reptiles on Pulau Tioman to 12.

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