Literature DB >> 11157002

A novel method for estimating substitution rate variation among sites in a large dataset of homologous DNA sequences.

G Pesole1, C Saccone.   

Abstract

We present here a novel method to estimate the site-specific relative variability in large sets of homologous sequences. It is based on the simple idea that the more closely related are the compared sequences, the higher the probability of observing nucleotide changes at rapidly evolving sites. A simulation study has been carried out to support the reliability of the method, which has been applied also to analyzing the site variability of all available human sequences corresponding to the two hypervariable regions of the mitochondrial D-loop.

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Year:  2001        PMID： 11157002      PMCID： PMC1461530     

Source DB:  PubMed          Journal:  Genetics        ISSN： 0016-6731            Impact factor:   4.562


  22 in total

1.  Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA.

Authors:  S Meyer; G Weiss; A von Haeseler
Journal:  Genetics       Date:  1999-07       Impact factor: 4.562

2.  Aging-dependent large accumulation of point mutations in the human mtDNA control region for replication.

Authors:  Y Michikawa; F Mazzucchelli; N Bresolin; G Scarlato; G Attardi
Journal:  Science       Date:  1999-10-22       Impact factor: 47.728

3.  Influence of base composition on quantitative estimates of gene evolution.

Authors:  C Saccone; C Lanave; G Pesole; G Preparata
Journal:  Methods Enzymol       Date:  1990       Impact factor: 1.600

4.  Estimating the pattern of nucleotide substitution.

Authors:  Z Yang
Journal:  J Mol Evol       Date:  1994-07       Impact factor: 2.395

5.  Sequence and organization of the human mitochondrial genome.

Authors:  S Anderson; A T Bankier; B G Barrell; M H de Bruijn; A R Coulson; J Drouin; I C Eperon; D P Nierlich; B A Roe; F Sanger; P H Schreier; A J Smith; R Staden; I G Young
Journal:  Nature       Date:  1981-04-09       Impact factor: 49.962

6.  Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees.

Authors:  L Excoffier; Z Yang
Journal:  Mol Biol Evol       Date:  1999-10       Impact factor: 16.240

7.  A new method for calculating evolutionary substitution rates.

Authors:  C Lanave; G Preparata; C Saccone; G Serio
Journal:  J Mol Evol       Date:  1984       Impact factor: 2.395

8.  The variability of the hepatitis B virus genome: statistical analysis and biological implications.

Authors:  I J Lauder; H J Lin; J Y Lau; T S Siu; C L Lai
Journal:  Mol Biol Evol       Date:  1993-03       Impact factor: 16.240

9.  Toward a more accurate time scale for the human mitochondrial DNA tree.

Authors:  M Hasegawa; A Di Rienzo; T D Kocher; A C Wilson
Journal:  J Mol Evol       Date:  1993-10       Impact factor: 2.395

10.  The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern.

Authors:  C Saccone; G Pesole; E Sbisá
Journal:  J Mol Evol       Date:  1991-07       Impact factor: 2.395
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  11 in total

1.  High-resolution genomic profiling of thyroid lesions uncovers preferential copy number gains affecting mitochondrial biogenesis loci in the oncocytic variants.

Authors:  Ivana Kurelac; Dario de Biase; Claudia Calabrese; Claudio Ceccarelli; Charlotte Ky Ng; Raymond Lim; Alan MacKay; Britta Weigelt; Anna Maria Porcelli; Jorge S Reis-Filho; Giovanni Tallini; Giuseppe Gasparre
Journal:  Am J Cancer Res       Date:  2015-05-15       Impact factor: 6.166

2.  Mutation hot spots in mammalian mitochondrial DNA.

Authors:  Nicolas Galtier; David Enard; Yoan Radondy; Eric Bazin; Khalid Belkhir
Journal:  Genome Res       Date:  2005-12-14       Impact factor: 9.043

3.  Correcting for purifying selection: an improved human mitochondrial molecular clock.

Authors:  Pedro Soares; Luca Ermini; Noel Thomson; Maru Mormina; Teresa Rito; Arne Röhl; Antonio Salas; Stephen Oppenheimer; Vincent Macaulay; Martin B Richards
Journal:  Am J Hum Genet       Date:  2009-06-04       Impact factor: 11.025

4.  Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation.

Authors:  Elizabeth M McCormick; Marie T Lott; Matthew C Dulik; Lishuang Shen; Marcella Attimonelli; Ornella Vitale; Amel Karaa; Renkui Bai; Daniel E Pineda-Alvarez; Larry N Singh; Christine M Stanley; Stacey Wong; Anshu Bhardwaj; Daria Merkurjev; Rong Mao; Neal Sondheimer; Shiping Zhang; Vincent Procaccio; Douglas C Wallace; Xiaowu Gai; Marni J Falk
Journal:  Hum Mutat       Date:  2020-11-10       Impact factor: 4.878

5.  HmtDB, a genomic resource for mitochondrion-based human variability studies.

Authors:  Francesco Rubino; Roberta Piredda; Francesco Maria Calabrese; Domenico Simone; Martin Lang; Claudia Calabrese; Vittoria Petruzzella; Mila Tommaseo-Ponzetta; Giuseppe Gasparre; Marcella Attimonelli
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

6.  HmtDB, a human mitochondrial genomic resource based on variability studies supporting population genetics and biomedical research.

Authors:  Marcella Attimonelli; Matteo Accetturo; Monica Santamaria; Daniela Lascaro; Gaetano Scioscia; Graziano Pappadà; Luigi Russo; Luigi Zanchetta; Mila Tommaseo-Ponzetta
Journal:  BMC Bioinformatics       Date:  2005-12-01       Impact factor: 3.169

7.  A multi-parametric workflow for the prioritization of mitochondrial DNA variants of clinical interest.

Authors:  Mariangela Santorsola; Claudia Calabrese; Giulia Girolimetti; Maria Angela Diroma; Giuseppe Gasparre; Marcella Attimonelli
Journal:  Hum Genet       Date:  2015-11-30       Impact factor: 4.132

8.  A comprehensive collection of annotations to interpret sequence variation in human mitochondrial transfer RNAs.

Authors:  Maria Angela Diroma; Paolo Lubisco; Marcella Attimonelli
Journal:  BMC Bioinformatics       Date:  2016-11-08       Impact factor: 3.169

9.  HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor.

Authors:  Rosanna Clima; Roberto Preste; Claudia Calabrese; Maria Angela Diroma; Mariangela Santorsola; Gaetano Scioscia; Domenico Simone; Lishuang Shen; Giuseppe Gasparre; Marcella Attimonelli
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

10.  Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates.

Authors:  Da-Peng Wang; Hao-Lei Wan; Song Zhang; Jun Yu
Journal:  Biol Direct       Date:  2009-06-16       Impact factor: 4.540
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