Literature DB >> 15342561

De novo repeat classification and fragment assembly.

Pavel A Pevzner1, Paul A Pevzner, Haixu Tang, Glenn Tesler.   

Abstract

Repetitive sequences make up a significant fraction of almost any genome, and an important and still open question in bioinformatics is how to represent all repeats in DNA sequences. We propose a new approach to repeat classification that represents all repeats in a genome as a mosaic of sub-repeats. Our key algorithmic idea also leads to new approaches to multiple alignment and fragment assembly. In particular, we show that our FragmentGluer assembler improves on Phrap and ARACHNE in assembly of BACs and bacterial genomes.

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Year:  2004        PMID： 15342561      PMCID： PMC515325          DOI： 10.1101/gr.2395204

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


  30 in total

1.  Estimating the repeat structure and length of DNA sequences using L-tuples.

Authors:  Xiaoman Li; Michael S Waterman
Journal:  Genome Res       Date:  2003-08       Impact factor: 9.043

2.  A contig assembly program based on sensitive detection of fragment overlaps.

Authors:  X Huang
Journal:  Genomics       Date:  1992-09       Impact factor: 5.736

3.  Human transaldolase-associated repetitive elements are transcribed by RNA polymerase III.

Authors:  A Perl; E Colombo; E Samoilova; M C Butler; K Banki
Journal:  J Biol Chem       Date:  2000-03-10       Impact factor: 5.157

4.  Multiple DNA and protein sequence alignment based on segment-to-segment comparison.

Authors:  B Morgenstern; A Dress; T Werner
Journal:  Proc Natl Acad Sci U S A       Date:  1996-10-29       Impact factor: 11.205

5.  A whole-genome assembly of Drosophila.

Authors:  E W Myers; G G Sutton; A L Delcher; I M Dew; D P Fasulo; M J Flanigan; S A Kravitz; C M Mobarry; K H Reinert; K A Remington; E L Anson; R A Bolanos; H H Chou; C M Jordan; A L Halpern; S Lonardi; E M Beasley; R C Brandon; L Chen; P J Dunn; Z Lai; Y Liang; D R Nusskern; M Zhan; Q Zhang; X Zheng; G M Rubin; M D Adams; J C Venter
Journal:  Science       Date:  2000-03-24       Impact factor: 47.728

6.  A new algorithm for DNA sequence assembly.

Authors:  R M Idury; M S Waterman
Journal:  J Comput Biol       Date:  1995       Impact factor: 1.479

7.  Toward simplifying and accurately formulating fragment assembly.

Authors:  E W Myers
Journal:  J Comput Biol       Date:  1995       Impact factor: 1.479

8.  An improved sequence assembly program.

Authors:  X Huang
Journal:  Genomics       Date:  1996-04-01       Impact factor: 5.736

9.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors:  J D Thompson; D G Higgins; T J Gibson
Journal:  Nucleic Acids Res       Date:  1994-11-11       Impact factor: 16.971

10.  Alignment of whole genomes.

Authors:  A L Delcher; S Kasif; R D Fleischmann; J Peterson; O White; S L Salzberg
Journal:  Nucleic Acids Res       Date:  1999-06-01       Impact factor: 16.971
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  70 in total

1.  SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Authors:  Anton Bankevich; Sergey Nurk; Dmitry Antipov; Alexey A Gurevich; Mikhail Dvorkin; Alexander S Kulikov; Valery M Lesin; Sergey I Nikolenko; Son Pham; Andrey D Prjibelski; Alexey V Pyshkin; Alexander V Sirotkin; Nikolay Vyahhi; Glenn Tesler; Max A Alekseyev; Pavel A Pevzner
Journal:  J Comput Biol       Date:  2012-04-16       Impact factor: 1.479

2.  Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers.

Authors:  Paul Medvedev; Son Pham; Mark Chaisson; Glenn Tesler; Pavel Pevzner
Journal:  J Comput Biol       Date:  2011-10-14       Impact factor: 1.479

3.  A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community.

Authors:  Mingjie Wang; Yuzhen Ye; Haixu Tang
Journal:  J Comput Biol       Date:  2012-06       Impact factor: 1.479

4.  Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition.

Authors:  Shu-Dan Yeh; Tiffanie Do; Carolus Chan; Adriana Cordova; Francisco Carranza; Eugene A Yamamoto; Mashya Abbassi; Kania A Gandasetiawan; Pablo Librado; Elisabetta Damia; Patrizio Dimitri; Julio Rozas; Daniel L Hartl; John Roote; José M Ranz
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-23       Impact factor: 11.205

5.  Reconstructing cancer genomes from paired-end sequencing data.

Authors:  Layla Oesper; Anna Ritz; Sarah J Aerni; Ryan Drebin; Benjamin J Raphael
Journal:  BMC Bioinformatics       Date:  2012-04-19       Impact factor: 3.169

6.  Short read fragment assembly of bacterial genomes.

Authors:  Mark J Chaisson; Pavel A Pevzner
Journal:  Genome Res       Date:  2007-12-14       Impact factor: 9.043

7.  De novo fragment assembly with short mate-paired reads: Does the read length matter?

Authors:  Mark J Chaisson; Dumitru Brinza; Pavel A Pevzner
Journal:  Genome Res       Date:  2008-12-03       Impact factor: 9.043

8.  Design of compact, universal DNA microarrays for protein binding microarray experiments.

Authors:  Anthony A Philippakis; Aaron M Qureshi; Michael F Berger; Martha L Bulyk
Journal:  J Comput Biol       Date:  2008-09       Impact factor: 1.479

9.  De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads.

Authors:  David Hernandez; Ryan Tewhey; Jean-Baptiste Veyrieras; Laurent Farinelli; Magne Østerås; Patrice François; Jacques Schrenzel
Journal:  Bioinformatics       Date:  2013-10-15       Impact factor: 6.937

10.  Maximum likelihood genome assembly.

Authors:  Paul Medvedev; Michael Brudno
Journal:  J Comput Biol       Date:  2009-08       Impact factor: 1.479
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