About: A novel fast vector method for genetic sequence comparison

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About: A novel fast vector method for genetic sequence comparison Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	A novel fast vector method for genetic sequence comparison
Creator	He, Lily Li, Yongkun He, Rong Yau, S.-T Stephen, &
Source	Medline; PMC
abstract	With sharp increasing in biological sequences, the traditional sequence alignment methods become unsuitable and infeasible. It motivates a surge of fast alignment-free techniques for sequence analysis. Among these methods, many sorts of feature vector methods are established and applied to reconstruction of species phylogeny. The vectors basically consist of some typical numerical features for certain biological problems. The features may come from the primary sequences, secondary or three dimensional structures of macromolecules. In this study, we propose a novel numerical vector based on only primary sequences of organism to build their phylogeny. Three chemical and physical properties of primary sequences: purine, pyrimidine and keto are also incorporated to the vector. Using each property, we convert the nucleotide sequence into a new sequence consisting of only two kinds of letters. Therefore, three sequences are constructed according to the three properties. For each letter of each sequence we calculate the number of the letter, the average position of the letter and the variation of the position of the letter appearing in the sequence. Tested on several datasets related to mammals, viruses and bacteria, this new tool is fast in speed and accurate for inferring the phylogeny of organisms.
has issue date	2017-09-22(xsd:dateTime)
bibo:doi	10.1038/s41598-017-12493-2
bibo:pmid	28939913
has license	cc-by
sha1sum (hex)	67773f5f18353fa2783c550d6c7fc52a2e10d0bc
schema:url	https://doi.org/10.1038/s41598-017-12493-2
resource representing a document's title	A novel fast vector method for genetic sequence comparison
has PubMed Central identifier	PMC5610321
has PubMed identifier	28939913
schema:publication	Sci Rep
resource representing a document's body	covid:67773f5f18353fa2783c550d6c7fc52a2e10d0bc#body_text
is schema:about of	named entity 'calculate' named entity 'sequence analysis' named entity 'Tested' named entity 'bacteria' named entity 'sorts' named entity 'basically' named entity 'SURGE' named entity 'LETTERS' named entity 'NUMERICAL' named entity 'CONSIST' named entity 'NOVEL' named entity 'SORTS' named entity 'VECTOR' named entity 'SPEED' named entity 'USING' named entity 'OF EACH' named entity 'ORGANISM' named entity 'MACROMOLECULES' named entity 'FEATURES' named entity 'BIOLOGICAL SEQUENCES' named entity 'AVERAGE' named entity 'FREE' named entity 'OPEN' named entity 'VECTOR' named entity 'FAST' named entity 'TYPICAL' named entity 'CHEMICAL AND PHYSICAL' named entity 'THESE' named entity 'SEQUENCE ALIGNMENT' named entity 'ESTABLISHED' named entity 'STUDY' named entity 'ACCURATE' named entity 'METHODS' named entity 'BUILD' named entity 'FEATURE' named entity 'PYRIMIDINE' named entity 'ALIGNMENT' named entity 'PRIMARY' named entity 'POSITION' named entity 'RECONSTRUCTION' named entity 'FAST' named entity 'THEIR' named entity 'SEQUENCES' named entity 'INFERRING' named entity 'SHARP' named entity 'APPLIED' named entity 'INCREASING' named entity 'LETTER' named entity 'BASED' named entity 'ACCORDING' named entity 'VIRUSES' named entity 'ORGANISMS' named entity 'NUMBER OF' named entity 'TECHNIQUES' named entity 'PROPERTIES' named entity 'VECTORS' named entity 'PROBLEMS' named entity 'VARIATION' named entity 'TRADITIONAL' named entity 'NOVEL' named entity 'CERTAIN' named entity 'SPECIES' named entity 'METHOD' named entity 'TOOL' named entity 'MAMMALS' named entity 'BIOLOGICAL' named entity 'PHYSICAL PROPERTIES' named entity 'COME' named entity 'RELATED' named entity 'NUCLEOTIDE SEQUENCE' named entity 'CONSTRUCTED' named entity 'KINDS' named entity 'PURINE' named entity 'THREE DIMENSIONAL' named entity 'BACTERIA' named entity 'SEQUENCE COMPARISON' named entity 'TESTED'

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