Literature DB >> 11337483

Directed gap closure in large-scale sequencing projects.

M Frohme1, A A Camargo, C Czink, A Y Matsukuma, A J Simpson, J D Hoheisel, S Verjovski-Almeida.   

Abstract

A problem in many sequencing projects is the final closure of gaps left in the clone libraries, which serve as templates for sequencing, because of uncloned or unclonable genomic areas. By use of the Xylella fastidiosa genome as a test system, we present here an approach to generate, in a directed manner, sequence information from those gaps. We suggest using the complete clone library as a competitor against the genomic DNA of interest in a subtractive hybridization procedure similar to representational difference analysis (RDA). The resulting sequence information can be used to screen selectively other clone resources or serve directly for gap closure.

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Year:  2001        PMID： 11337483      PMCID： PMC311138          DOI： 10.1101/gr.179401

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


  8 in total

1.  The DNA sequence of human chromosome 21.

Authors:  M Hattori; A Fujiyama; T D Taylor; H Watanabe; T Yada; H S Park; A Toyoda; K Ishii; Y Totoki; D K Choi; Y Groner; E Soeda; M Ohki; T Takagi; Y Sakaki; S Taudien; K Blechschmidt; A Polley; U Menzel; J Delabar; K Kumpf; R Lehmann; D Patterson; K Reichwald; A Rump; M Schillhabel; A Schudy; W Zimmermann; A Rosenthal; J Kudoh; K Schibuya; K Kawasaki; S Asakawa; A Shintani; T Sasaki; K Nagamine; S Mitsuyama; S E Antonarakis; S Minoshima; N Shimizu; G Nordsiek; K Hornischer; P Brant; M Scharfe; O Schon; A Desario; J Reichelt; G Kauer; H Blocker; J Ramser; A Beck; S Klages; S Hennig; L Riesselmann; E Dagand; T Haaf; S Wehrmeyer; K Borzym; K Gardiner; D Nizetic; F Francis; H Lehrach; R Reinhardt; M L Yaspo
Journal:  Nature       Date:  2000-05-18       Impact factor: 49.962

2.  Mapping analysis of the Xylella fastidiosa genome.

Authors:  M Frohme; A A Camargo; S Heber; C Czink; A J Simpson; J D Hoheisel; A P de Souza
Journal:  Nucleic Acids Res       Date:  2000-08-15       Impact factor: 16.971

3.  Cloning the differences between two complex genomes.

Authors:  N Lisitsyn; N Lisitsyn; M Wigler
Journal:  Science       Date:  1993-02-12       Impact factor: 47.728

4.  Identifying differences in mRNA expression by representational difference analysis of cDNA.

Authors:  M Hubank; D G Schatz
Journal:  Nucleic Acids Res       Date:  1994-12-25       Impact factor: 16.971

5.  The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis.

Authors:  A J Simpson; F C Reinach; P Arruda; F A Abreu; M Acencio; R Alvarenga; L M Alves; J E Araya; G S Baia; C S Baptista; M H Barros; E D Bonaccorsi; S Bordin; J M Bové; M R Briones; M R Bueno; A A Camargo; L E Camargo; D M Carraro; H Carrer; N B Colauto; C Colombo; F F Costa; M C Costa; C M Costa-Neto; L L Coutinho; M Cristofani; E Dias-Neto; C Docena; H El-Dorry; A P Facincani; A J Ferreira; V C Ferreira; J A Ferro; J S Fraga; S C França; M C Franco; M Frohme; L R Furlan; M Garnier; G H Goldman; M H Goldman; S L Gomes; A Gruber; P L Ho; J D Hoheisel; M L Junqueira; E L Kemper; J P Kitajima; J E Krieger; E E Kuramae; F Laigret; M R Lambais; L C Leite; E G Lemos; M V Lemos; S A Lopes; C R Lopes; J A Machado; M A Machado; A M Madeira; H M Madeira; C L Marino; M V Marques; E A Martins; E M Martins; A Y Matsukuma; C F Menck; E C Miracca; C Y Miyaki; C B Monteriro-Vitorello; D H Moon; M A Nagai; A L Nascimento; L E Netto; A Nhani; F G Nobrega; L R Nunes; M A Oliveira; M C de Oliveira; R C de Oliveira; D A Palmieri; A Paris; B R Peixoto; G A Pereira; H A Pereira; J B Pesquero; R B Quaggio; P G Roberto; V Rodrigues; A J de M Rosa; V E de Rosa; R G de Sá; R V Santelli; H E Sawasaki; A C da Silva; A M da Silva; F R da Silva; W A da Silva; J F da Silveira; M L Silvestri; W J Siqueira; A A de Souza; A P de Souza; M F Terenzi; D Truffi; S M Tsai; M H Tsuhako; H Vallada; M A Van Sluys; S Verjovski-Almeida; A L Vettore; M A Zago; M Zatz; J Meidanis; J C Setubal
Journal:  Nature       Date:  2000-07-13       Impact factor: 49.962

6.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

Authors:  R D Fleischmann; M D Adams; O White; R A Clayton; E F Kirkness; A R Kerlavage; C J Bult; J F Tomb; B A Dougherty; J M Merrick
Journal:  Science       Date:  1995-07-28       Impact factor: 47.728

Review 7.  Genome sequence of the nematode C. elegans: a platform for investigating biology.

Authors: 
Journal:  Science       Date:  1998-12-11       Impact factor: 47.728

8.  The genome sequence of Drosophila melanogaster.

Authors:  M D Adams; S E Celniker; R A Holt; C A Evans; J D Gocayne; P G Amanatides; S E Scherer; P W Li; R A Hoskins; R F Galle; R A George; S E Lewis; S Richards; M Ashburner; S N Henderson; G G Sutton; J R Wortman; M D Yandell; Q Zhang; L X Chen; R C Brandon; Y H Rogers; R G Blazej; M Champe; B D Pfeiffer; K H Wan; C Doyle; E G Baxter; G Helt; C R Nelson; G L Gabor; J F Abril; A Agbayani; H J An; C Andrews-Pfannkoch; D Baldwin; R M Ballew; A Basu; J Baxendale; L Bayraktaroglu; E M Beasley; K Y Beeson; P V Benos; B P Berman; D Bhandari; S Bolshakov; D Borkova; M R Botchan; J Bouck; P Brokstein; P Brottier; K C Burtis; D A Busam; H Butler; E Cadieu; A Center; I Chandra; J M Cherry; S Cawley; C Dahlke; L B Davenport; P Davies; B de Pablos; A Delcher; Z Deng; A D Mays; I Dew; S M Dietz; K Dodson; L E Doup; M Downes; S Dugan-Rocha; B C Dunkov; P Dunn; K J Durbin; C C Evangelista; C Ferraz; S Ferriera; W Fleischmann; C Fosler; A E Gabrielian; N S Garg; W M Gelbart; K Glasser; A Glodek; F Gong; J H Gorrell; Z Gu; P Guan; M Harris; N L Harris; D Harvey; T J Heiman; J R Hernandez; J Houck; D Hostin; K A Houston; T J Howland; M H Wei; C Ibegwam; M Jalali; F Kalush; G H Karpen; Z Ke; J A Kennison; K A Ketchum; B E Kimmel; C D Kodira; C Kraft; S Kravitz; D Kulp; Z Lai; P Lasko; Y Lei; A A Levitsky; J Li; Z Li; Y Liang; X Lin; X Liu; B Mattei; T C McIntosh; M P McLeod; D McPherson; G Merkulov; N V Milshina; C Mobarry; J Morris; A Moshrefi; S M Mount; M Moy; B Murphy; L Murphy; D M Muzny; D L Nelson; D R Nelson; K A Nelson; K Nixon; D R Nusskern; J M Pacleb; M Palazzolo; G S Pittman; S Pan; J Pollard; V Puri; M G Reese; K Reinert; K Remington; R D Saunders; F Scheeler; H Shen; B C Shue; I Sidén-Kiamos; M Simpson; M P Skupski; T Smith; E Spier; A C Spradling; M Stapleton; R Strong; E Sun; R Svirskas; C Tector; R Turner; E Venter; A H Wang; X Wang; Z Y Wang; D A Wassarman; G M Weinstock; J Weissenbach; S M Williams; K C Worley; D Wu; S Yang; Q A Yao; J Ye; R F Yeh; J S Zaveri; M Zhan; G Zhang; Q Zhao; L Zheng; X H Zheng; F N Zhong; W Zhong; X Zhou; S Zhu; X Zhu; H O Smith; R A Gibbs; E W Myers; G M Rubin; J C Venter
Journal:  Science       Date:  2000-03-24       Impact factor: 47.728
  8 in total
  1 in total

1.  Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing.

Authors:  Tae-Jin Yang; Yeisoo Yu; Gyoungju Nah; Michael Atkins; Seunghee Lee; David A Frisch; Rod A Wing
Journal:  Theor Appl Genet       Date:  2003-06-03       Impact factor: 5.699
  1 in total

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