Literature DB >> 493154

Computer programs for the assembly of DNA sequences.

T R Gingeras, J P Milazzo, D Sciaky, R J Roberts.   

Abstract

A collection of user-interactive computer programs is described which aid in the assembly of DNA sequences. This is achieved by searching for the positions of overlapping common nucleotide sequences within the blocks of sequence obtained as primary data. Such overlapping segments are then melded into one continuous string of nucleotides. Strategies for determining the accuracy of the sequence being analyzed and reducing the error rate resulting from the manual manipulation of sequence data are discussed. Sequences mapping from 97.3 to 100% of the Ad2 virus genome were used to demonstrate the performance of these programs.

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Year:  1979        PMID： 493154      PMCID： PMC328034          DOI： 10.1093/nar/7.2.529

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  9 in total

1.  Cleavage maps of DNA from adenovirus types 2 and 5 by restriction endonucleases EcoRI and HpaI.

Authors:  C Mulder; J R Arrand; H Delius; W Keller; U Pettersson; R J Roberts; P A Sharp
Journal:  Cold Spring Harb Symp Quant Biol       Date:  1975

2.  The genome of simian virus 40.

Authors:  V B Reddy; B Thimmappaya; R Dhar; K N Subramanian; B S Zain; J Pan; P K Ghosh; M L Celma; S M Weissman
Journal:  Science       Date:  1978-05-05       Impact factor: 47.728

3.  Complete nucleotide sequence of SV40 DNA.

Authors:  W Fiers; R Contreras; G Haegemann; R Rogiers; A Van de Voorde; H Van Heuverswyn; J Van Herreweghe; G Volckaert; M Ysebaert
Journal:  Nature       Date:  1978-05-11       Impact factor: 49.962

4.  Nucleotide sequence of bacteriophage phi X174 DNA.

Authors:  F Sanger; G M Air; B G Barrell; N L Brown; A R Coulson; C A Fiddes; C A Hutchison; P M Slocombe; M Smith
Journal:  Nature       Date:  1977-02-24       Impact factor: 49.962

5.  A new method for sequencing DNA.

Authors:  A M Maxam; W Gilbert
Journal:  Proc Natl Acad Sci U S A       Date:  1977-02       Impact factor: 11.205

6.  Computer analysis of nucleic acid regulatory sequences.

Authors:  L J Korn; C L Queen; M N Wegman
Journal:  Proc Natl Acad Sci U S A       Date:  1977-10       Impact factor: 11.205

7.  A simple method for DNA restriction site mapping.

Authors:  H O Smith; M L Birnstiel
Journal:  Nucleic Acids Res       Date:  1976-09       Impact factor: 16.971

8.  Sequence data handling by computer.

Authors:  R Staden
Journal:  Nucleic Acids Res       Date:  1977-11       Impact factor: 16.971

9.  DNA sequencing with chain-terminating inhibitors.

Authors:  F Sanger; S Nicklen; A R Coulson
Journal:  Proc Natl Acad Sci U S A       Date:  1977-12       Impact factor: 11.205
  9 in total
  32 in total

1.  Finding errors in DNA sequences.

Authors:  J Posfai; R J Roberts
Journal:  Proc Natl Acad Sci U S A       Date:  1992-05-15       Impact factor: 11.205

2.  New Generations: Sequencing Machines and Their Computational Challenges.

Authors:  David C Schwartz; Michael S Waterman
Journal:  J Comput Sci Technol       Date:  2010-01-01       Impact factor: 1.571

3.  Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly.

Authors:  Heng Li
Journal:  Bioinformatics       Date:  2012-05-07       Impact factor: 6.937

4.  Cloning and characterization of the HpaII methylase gene.

Authors:  C O Card; G G Wilson; K Weule; J Hasapes; A Kiss; R J Roberts
Journal:  Nucleic Acids Res       Date:  1990-03-25       Impact factor: 16.971

5.  A comprehensive package for DNA sequence analysis in FORTRAN IV for the PDP-11.

Authors:  J Arnold; V K Eckenrode; K Lemke; G J Phillips; S W Schaeffer
Journal:  Nucleic Acids Res       Date:  1986-01-10       Impact factor: 16.971

6.  Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products.

Authors:  G Theriault; P H Roy; K A Howard; J S Benner; J E Brooks; A F Waters; T R Gingeras
Journal:  Nucleic Acids Res       Date:  1985-12-09       Impact factor: 16.971

7.  Cloning and characterization of the genes encoding the MspI restriction modification system.

Authors:  P M Lin; C H Lee; R J Roberts
Journal:  Nucleic Acids Res       Date:  1989-04-25       Impact factor: 16.971

8.  DNA sequence analysis: a procedure to find homologies among many sequences.

Authors:  G Krishnan; R K Kaul; P Jagadeeswaran
Journal:  Nucleic Acids Res       Date:  1986-01-10       Impact factor: 16.971

9.  Assembly of overlapping DNA sequences by a program written in BASIC for 64K CP/M and MS-DOS IBM-compatible microcomputers.

Authors:  R E Johnston; J M Mackenzie; W G Dougherty
Journal:  Nucleic Acids Res       Date:  1986-01-10       Impact factor: 16.971

10.  Nucleotide sequence of the 3' end of MCF 247 murine leukemia virus.

Authors:  M Kelly; C A Holland; M L Lung; S K Chattopadhyay; D R Lowy; N H Hopkins
Journal:  J Virol       Date:  1983-01       Impact factor: 5.103
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