About: A rebuttal to the comments on the genome order index and the Z-curve

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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 rebuttal to the comments on the genome order index and the Z-curve
Creator	Zhang, Ren
Source	Medline; PMC
abstract	BACKGROUND: Elhaik, Graur and Josic recently commented on the genome order index (S) and the Z-curve (Elhaik et al. Biol Direct 2010, 5: 10). S is a quantity defined as S = a(2 )+ c(2 )+ g(2 )+ t(2), where a, c, g and t denote corresponding base frequencies. The Z-curve is a three dimensional curve that represents a DNA sequence in the manner that each can be uniquely reconstructed given the other. Elhaik et al. made 4 major claims. 1) In the previous mapping system with the regular tetrahedron, calculation of the radius of the inscribed sphere is %22a mathematical error%22. 2) S follows an exponential distribution and is narrowly distributed with a range of (0.25 - 0.33). 3) Based on the Chargaff's second parity rule (PR2), %22S is equivalent to H [Shannon entropy]%22 and they are derivable from each other. 4) Z-curve %22suffers from over dimensionality%22, because based on the analysis of 235 bacterial genomes, x and y components contributed only less than 1% of the variance and therefore %22would be of little use%22. RESULTS: 1) Elhaik et al. mistakenly neglected the parameter [Formula: see text] when calculating the radius of the inscribed sphere. 2) The exponential distribution of S is a restatement of our previous conclusion, and the range of (0.25 - 0.33) only paraphrases the previously suggested S range (0.25 -1/3). 3) Elhaik et al. incorrectly disregard deviations from PR2 by treating the deviations as 0 altogether, reduce S and H, both having 4 variables, a, c, g and t, into functions of one single variable, a only, and apply this treatment to all DNA sequences as the basis of their %22demonstration%22, which is therefore invalid. 4) Elhaik et al. confuse numeral smallness with biological insignificance, and disregard the distributions of purine/pyrimidine and amino/keto bases (x and y components), the variations of which, although can be less than that of GC content, contain rich information that is important and useful, such as in locating replication origins of bacterial and archaeal genomes, and in studies of gene recognition in various species. CONCLUSION: Elhaik et al. confuse S (a single number) with Z-curve (a series of 3D coordinates), which are distinct. To use S as a case study of Z-curve, by itself, is invalid. S and H are neither equivalent nor derivable from each other. The criticisms of Elhaik, Graur and Josic are wrong. REVIEWERS: This article was reviewed by Erik van Nimwegen.
has issue date	2011-02-16(xsd:dateTime)
bibo:doi	10.1186/1745-6150-6-10
bibo:pmid	21324187
has license	cc-by
sha1sum (hex)	5cd3d3edd1b68bce986c6b9e6bfa9720efd041e3
schema:url	https://doi.org/10.1186/1745-6150-6-10
resource representing a document's title	A rebuttal to the comments on the genome order index and the Z-curve
has PubMed Central identifier	PMC3046898
has PubMed identifier	21324187
schema:publication	Biol Direct
resource representing a document's body	covid:5cd3d3edd1b68bce986c6b9e6bfa9720efd041e3#body_text
is schema:about of	named entity 'order' named entity 'distributed' named entity 'major' named entity 'FREQUENCIES' named entity 'INDEX' named entity 'RECENTLY' named entity 'DNA SEQUENCE' named entity 'THREE DIMENSIONAL' named entity 'RANGE' named entity 'CURVE' named entity 'RECONSTRUCTED' named entity 'MAPPING' named entity 'USE' named entity 'DIMENSIONALITY' named entity 'GENOME' named entity 'REGULAR' named entity 'GIVEN' named entity 'BACKGROUND' named entity 'ORDER' named entity 'ANALYSIS' named entity 'FOLLOWS' named entity 'COMMENTS' named entity 'MATHEMATICAL' named entity 'DEFINED' named entity 'LESS THAN' named entity 'LITTLE' named entity 'A DNA' named entity 'ORDER' named entity 'GENOME' named entity 'MAJOR' named entity 'PREVIOUS' named entity 'DISTRIBUTED' named entity 'TETRAHEDRON' named entity 'WHERE' named entity 'G 2' named entity '28S' named entity 'SYSTEM' named entity 'INDEX' named entity '27S' named entity 'VARIANCE' named entity 'CALCULATION' named entity 'EQUIVALENT' named entity 'EXPONENTIAL DISTRIBUTION' named entity 'ENTROPY' named entity 'DIRECT' named entity 'C 2' named entity '0.33' named entity '22A' named entity 'PARITY' named entity 'RULE' named entity 'SECOND' named entity '22S' named entity 'BASED' named entity 'ERROR' named entity 'RADIUS' named entity 'BACTERIAL GENOMES' named entity 'QUANTITY' named entity 'IS A' named entity 'COMPONENTS' named entity '10%' named entity 'SPHERE' named entity 'BASE' named entity 'CURVE' named entity 'genome' named entity 'calculation' named entity 'claims' named entity 'Shannon entropy' named entity 'Chargaff's second parity rule' named entity 'defined' named entity 'Josic' named entity 'genomes' named entity 'GC content' named entity 'GC-content' named entity 'GC-content' named entity 'human genome' named entity 'DNA sequences' named entity 'Aeropyrum pernix' named entity 'DNA sequences' named entity 'genome' named entity 'DNA sequence' named entity 'genome'

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