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Literature DB >> 12466299

Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencing.

Abstract

We develop an extension to the Lander-Waterman theory for characterizing gaps in bacterial artificial chromosome fingerprint mapping and shotgun sequencing projects. It supports a larger set of descriptive statistics and is applicable to a wider range of project parameters. We show that previous assertions regarding inconsistency of the Lander-Waterman theory at higher coverages are incorrect and that another well-known but ostensibly different model is in fact the same. The apparent paradox of infinite island lengths is resolved. Several applications are shown, including evolution of the probability density function, calculation of closure probabilities, and development of a probabilistic method for computing stopping points in bacterial artificial chromosome shotgun sequencing.

Mesh：

Substances：
DNA, Bacterial

Year: 2002 PMID： 12466299 PMCID： PMC187573 DOI： 10.1101/gr.655102

Source DB: PubMed Journal: Genome Res ISSN： 1088-9051 Impact factor: 9.043

37 in total

1. Theories and applications for sequencing randomly selected clones.

Authors: M C Wendl; M A Marra; L W Hillier; A T Chinwalla; R K Wilson; R H Waterston
Journal: Genome Res Date: 2001-02 Impact factor: 9.043

2. Initial sequencing and analysis of the human genome.

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Journal: Nature Date: 2001-02-15 Impact factor: 49.962

3. A physical map of the human genome.

Authors: J D McPherson; M Marra; L Hillier; R H Waterston; A Chinwalla; J Wallis; M Sekhon; K Wylie; E R Mardis; R K Wilson; R Fulton; T A Kucaba; C Wagner-McPherson; W B Barbazuk; S G Gregory; S J Humphray; L French; R S Evans; G Bethel; A Whittaker; J L Holden; O T McCann; A Dunham; C Soderlund; C E Scott; D R Bentley; G Schuler; H C Chen; W Jang; E D Green; J R Idol; V V Maduro; K T Montgomery; E Lee; A Miller; S Emerling; R Gibbs; S Scherer; J H Gorrell; E Sodergren; K Clerc-Blankenburg; P Tabor; S Naylor; D Garcia; P J de Jong; J J Catanese; N Nowak; K Osoegawa; S Qin; L Rowen; A Madan; M Dors; L Hood; B Trask; C Friedman; H Massa; V G Cheung; I R Kirsch; T Reid; R Yonescu; J Weissenbach; T Bruls; R Heilig; E Branscomb; A Olsen; N Doggett; J F Cheng; T Hawkins; R M Myers; J Shang; L Ramirez; J Schmutz; O Velasquez; K Dixon; N E Stone; D R Cox; D Haussler; W J Kent; T Furey; S Rogic; S Kennedy; S Jones; A Rosenthal; G Wen; M Schilhabel; G Gloeckner; G Nyakatura; R Siebert; B Schlegelberger; J Korenberg; X N Chen; A Fujiyama; M Hattori; A Toyoda; T Yada; H S Park; Y Sakaki; N Shimizu; S Asakawa; K Kawasaki; T Sasaki; A Shintani; A Shimizu; K Shibuya; J Kudoh; S Minoshima; J Ramser; P Seranski; C Hoff; A Poustka; R Reinhardt; H Lehrach
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

4. A complete BAC-based physical map of the Arabidopsis thaliana genome.

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Journal: Nat Genet Date: 1999-07 Impact factor: 38.330

5. Physical map and organization of chromosome 7 in the rice blast fungus, Magnaporthe grisea.

Authors: H Zhu; B P Blackmon; M Sasinowski; R A Dean
Journal: Genome Res Date: 1999-08 Impact factor: 9.043

6. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

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Journal: Nature Date: 2000-12-14 Impact factor: 49.962

7. Genomic organization, chromosomal localization, and the complete 22 kb DNA sequence of the human GCMa/GCM1, a placenta-specific transcription factor gene.

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Journal: Biochem Biophys Res Commun Date: 2000-11-11 Impact factor: 3.575

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Journal: Science Date: 2001-02-16 Impact factor: 47.728

9. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.

Authors: J F Heidelberg; J A Eisen; W C Nelson; R A Clayton; M L Gwinn; R J Dodson; D H Haft; E K Hickey; J D Peterson; L Umayam; S R Gill; K E Nelson; T D Read; H Tettelin; D Richardson; M D Ermolaeva; J Vamathevan; S Bass; H Qin; I Dragoi; P Sellers; L McDonald; T Utterback; R D Fleishmann; W C Nierman; O White; S L Salzberg; H O Smith; R R Colwell; J J Mekalanos; J C Venter; C M Fraser
Journal: Nature Date: 2000-08-03 Impact factor: 49.962

10. Integration of cytogenetic landmarks into the draft sequence of the human genome.

Authors: V G Cheung; N Nowak; W Jang; I R Kirsch; S Zhao; X N Chen; T S Furey; U J Kim; W L Kuo; M Olivier; J Conroy; A Kasprzyk; H Massa; R Yonescu; S Sait; C Thoreen; A Snijders; E Lemyre; J A Bailey; A Bruzel; W D Burrill; S M Clegg; S Collins; P Dhami; C Friedman; C S Han; S Herrick; J Lee; A H Ligon; S Lowry; M Morley; S Narasimhan; K Osoegawa; Z Peng; I Plajzer-Frick; B J Quade; D Scott; K Sirotkin; A A Thorpe; J W Gray; J Hudson; D Pinkel; T Ried; L Rowen; G L Shen-Ong; R L Strausberg; E Birney; D F Callen; J F Cheng; D R Cox; N A Doggett; N P Carter; E E Eichler; D Haussler; J R Korenberg; C C Morton; D Albertson; G Schuler; P J de Jong; B J Trask
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

12 in total

1. The international barley sequencing consortium--at the threshold of efficient access to the barley genome.

Authors: Daniela Schulte; Timothy J Close; Andreas Graner; Peter Langridge; Takashi Matsumoto; Gary Muehlbauer; Kazuhiro Sato; Alan H Schulman; Robbie Waugh; Roger P Wise; Nils Stein
Journal: Plant Physiol Date: 2009-01 Impact factor: 8.340

2. Efficient study design for next generation sequencing.

Authors: Joshua Sampson; Kevin Jacobs; Meredith Yeager; Stephen Chanock; Nilanjan Chatterjee
Journal: Genet Epidemiol Date: 2011-05 Impact factor: 2.135

3. Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.

Authors: Matt J Cahill; Claudio U Köser; Nicholas E Ross; John A C Archer
Journal: PLoS One Date: 2010-07-12 Impact factor: 3.240

4. Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem.

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Journal: J Math Biol Date: 2012-09-11 Impact factor: 2.259

5. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

Authors: David Hernandez; Patrice François; Laurent Farinelli; Magne Osterås; Jacques Schrenzel
Journal: Genome Res Date: 2008-03-10 Impact factor: 9.043

6. Extension of Lander-Waterman theory for sequencing filtered DNA libraries.

Authors: Michael C Wendl; W Brad Barbazuk
Journal: BMC Bioinformatics Date: 2005-10-10 Impact factor: 3.169

7. Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: theory and practical application to genomic and metagenomic projects.

Authors: John Moriarty; Julian R Marchesi; Anthony Metcalfe
Journal: BMC Bioinformatics Date: 2007-03-02 Impact factor: 3.169

8. Statistical aspects of discerning indel-type structural variation via DNA sequence alignment.

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9. Separating metagenomic short reads into genomes via clustering.

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Journal: Algorithms Mol Biol Date: 2012-09-26 Impact factor: 1.405

10. A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao.

Authors: Jorge M C Mondego; Marcelo F Carazzolle; Gustavo G L Costa; Eduardo F Formighieri; Lucas P Parizzi; Johana Rincones; Carolina Cotomacci; Dirce M Carraro; Anderson F Cunha; Helaine Carrer; Ramon O Vidal; Raíssa C Estrela; Odalys García; Daniela P T Thomazella; Bruno V de Oliveira; Acássia Bl Pires; Maria Carolina S Rio; Marcos Renato R Araújo; Marcos H de Moraes; Luis A B Castro; Karina P Gramacho; Marilda S Gonçalves; José P Moura Neto; Aristóteles Góes Neto; Luciana V Barbosa; Mark J Guiltinan; Bryan A Bailey; Lyndel W Meinhardt; Julio Cm Cascardo; Gonçalo A G Pereira
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