Literature DB >> 7063399

Codon preference and its use in identifying protein coding regions in long DNA sequences.

R Staden, A D McLachlan.   

Abstract

This paper describes a computer method that uses codon preference to help find protein coding regions in long DNA sequences. The method can distinguish between introns and exons and can help to detect sequencing errors.

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Substances：

Year:  1982        PMID： 7063399      PMCID： PMC326122          DOI： 10.1093/nar/10.1.141

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


  11 in total

1.  Molecular analysis of the unc-54 myosin heavy-chain gene of Caenorhabditis elegans.

Authors:  A R MacLeod; J Karn; S Brenner
Journal:  Nature       Date:  1981-06-04       Impact factor: 49.962

2.  Nucleotide sequence of bacteriophage G4 DNA.

Authors:  G N Godson; B G Barrell; R Staden; J C Fiddes
Journal:  Nature       Date:  1978-11-16       Impact factor: 49.962

3.  The coding function of nucleotide sequences can be discerned by statistical analysis.

Authors:  M J Shulman; C M Steinberg; N Westmoreland
Journal:  J Theor Biol       Date:  1981-02-07       Impact factor: 2.691

Review 4.  Codon catalog usage and the genome hypothesis.

Authors:  R Grantham; C Gautier; M Gouy; R Mercier; A Pavé
Journal:  Nucleic Acids Res       Date:  1980-01-11       Impact factor: 16.971

5.  Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification.

Authors:  J C Shepherd
Journal:  Proc Natl Acad Sci U S A       Date:  1981-03       Impact factor: 11.205

6.  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

7.  Preferential codon usage in genes.

Authors:  S Wain-Hobson; R Nussinov; R J Brown; J L Sussman
Journal:  Gene       Date:  1981-05       Impact factor: 3.688

8.  A computer program to search for tRNA genes.

Authors:  R Staden
Journal:  Nucleic Acids Res       Date:  1980-02-25       Impact factor: 16.971

9.  Some rules in the ordering of nucleotides in the DNA.

Authors:  R Nussinov
Journal:  Nucleic Acids Res       Date:  1980-10-10       Impact factor: 16.971

10.  Nucleotide sequence of bacteriophage fd DNA.

Authors:  E Beck; R Sommer; E A Auerswald; C Kurz; B Zink; G Osterburg; H Schaller; K Sugimoto; H Sugisaki; T Okamoto; M Takanami
Journal:  Nucleic Acids Res       Date:  1978-12       Impact factor: 16.971
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  171 in total

1.  The genome of turkey herpesvirus.

Authors:  C L Afonso; E R Tulman; Z Lu; L Zsak; D L Rock; G F Kutish
Journal:  J Virol       Date:  2001-01       Impact factor: 5.103

2.  Identification and analysis of the balhimycin biosynthetic gene cluster and its use for manipulating glycopeptide biosynthesis in Amycolatopsis mediterranei DSM5908.

Authors:  S Pelzer; R Süssmuth; D Heckmann; J Recktenwald; P Huber; G Jung; W Wohlleben
Journal:  Antimicrob Agents Chemother       Date:  1999-07       Impact factor: 5.191

3.  Genome sequence of a baculovirus pathogenic for Culex nigripalpus.

Authors:  C L Afonso; E R Tulman; Z Lu; C A Balinsky; B A Moser; J J Becnel; D L Rock; G F Kutish
Journal:  J Virol       Date:  2001-11       Impact factor: 5.103

4.  The genome of a very virulent Marek's disease virus.

Authors:  E R Tulman; C L Afonso; Z Lu; L Zsak; D L Rock; G F Kutish
Journal:  J Virol       Date:  2000-09       Impact factor: 5.103

5.  Gene prediction by spectral rotation measure: a new method for identifying protein-coding regions.

Authors:  Daniel Kotlar; Yizhar Lavner
Journal:  Genome Res       Date:  2003-07-17       Impact factor: 9.043

6.  Biosynthetic gene cluster of the herbicide phosphinothricin tripeptide from Streptomyces viridochromogenes Tü494.

Authors:  Dirk Schwartz; Susanne Berger; Eva Heinzelmann; Konstanze Muschko; Kathrin Welzel; Wolfgang Wohlleben
Journal:  Appl Environ Microbiol       Date:  2004-12       Impact factor: 4.792

7.  Genome of bovine herpesvirus 5.

Authors:  G Delhon; M P Moraes; Z Lu; C L Afonso; E F Flores; R Weiblen; G F Kutish; D L Rock
Journal:  J Virol       Date:  2003-10       Impact factor: 5.103

8.  Open reading frame 5 (ORF5), encoding a ferredoxinlike protein, and nifQ are cotranscribed with nifE, nifN, nifX, and ORF4 in Rhodobacter capsulatus.

Authors:  C Moreno-Vivian; S Hennecke; A Pühler; W Klipp
Journal:  J Bacteriol       Date:  1989-05       Impact factor: 3.490

9.  Nucleotide sequence encoding the iron-sulphur protein subunit of the succinate dehydrogenase of Escherichia coli.

Authors:  M G Darlison; J R Guest
Journal:  Biochem J       Date:  1984-10-15       Impact factor: 3.857

10.  Nucleotide sequence of the Rhodospirillum rubrum atp operon.

Authors:  G Falk; A Hampe; J E Walker
Journal:  Biochem J       Date:  1985-06-01       Impact factor: 3.857
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