Literature DB >> 6694906

The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression.

M Gribskov, J Devereux, R R Burgess.   

Abstract

The codon preference plot is useful for locating genes in sequenced DNA, predicting the relative level of their expression and for detecting DNA sequencing errors resulting in the insertion or deletion of bases within a coding sequence. The three possible reading frames are displayed in parallel along with the open reading frames and plots of the location of rare codons in each reading frame.

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Year:  1984        PMID： 6694906      PMCID： PMC321069          DOI： 10.1093/nar/12.1part2.539

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


  19 in total

1.  Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli.

Authors:  L E Post; G D Strycharz; M Nomura; H Lewis; P P Dennis
Journal:  Proc Natl Acad Sci U S A       Date:  1979-04       Impact factor: 11.205

2.  Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type.

Authors:  R Grantham; C Gautier; M Gouy
Journal:  Nucleic Acids Res       Date:  1980-05-10       Impact factor: 16.971

3.  The primary structure of Escherichia coli RNA polymerase. Nucleotide sequence of the rpoB gene and amino-acid sequence of the beta-subunit.

Authors:  Y A Ovchinnikov; G S Monastyrskaya; V V Gubanov; S O Guryev; N N Modyanov; V A Grinkevich; I A Makarova; T V Marchenko; I N Polovnikova; V M Lipkin; E D Sverdlov
Journal:  Eur J Biochem       Date:  1981-06-01

4.  Codon usage in bacteria: correlation with gene expressivity.

Authors:  M Gouy; C Gautier
Journal:  Nucleic Acids Res       Date:  1982-11-25       Impact factor: 16.971

Review 5.  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

6.  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

7.  Biosynthesis of RNA polymerase in Escherichia coli. I. Control of RNA polymerase content at various growth rates.

Authors:  Y Iwakura; K Ito; A Ishihama
Journal:  Mol Gen Genet       Date:  1974

8.  Codon catalog usage is a genome strategy modulated for gene expressivity.

Authors:  R Grantham; C Gautier; M Gouy; M Jacobzone; R Mercier
Journal:  Nucleic Acids Res       Date:  1981-01-10       Impact factor: 16.971

9.  Recognition of protein coding regions in DNA sequences.

Authors:  J W Fickett
Journal:  Nucleic Acids Res       Date:  1982-09-11       Impact factor: 16.971

10.  Primase, the dnaG protein of Escherichia coli. An enzyme which starts DNA chains.

Authors:  L Rowen; A Kornberg
Journal:  J Biol Chem       Date:  1978-02-10       Impact factor: 5.157
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  141 in total

1.  Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence.

Authors:  C Médigue; M Rose; A Viari; A Danchin
Journal:  Genome Res       Date:  1999-11       Impact factor: 9.043

2.  GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

Authors:  J Besemer; A Lomsadze; M Borodovsky
Journal:  Nucleic Acids Res       Date:  2001-06-15       Impact factor: 16.971

3.  A DnaB intein in Rhodothermus marinus: indication of recent intein homing across remotely related organisms.

Authors:  X Q Liu; Z Hu
Journal:  Proc Natl Acad Sci U S A       Date:  1997-07-22       Impact factor: 11.205

4.  HeT-A, a transposable element specifically involved in "healing" broken chromosome ends in Drosophila melanogaster.

Authors:  H Biessmann; K Valgeirsdottir; A Lofsky; C Chin; B Ginther; R W Levis; M L Pardue
Journal:  Mol Cell Biol       Date:  1992-09       Impact factor: 4.272

5.  Identification of an operon involved in sulfolipid biosynthesis in Rhodobacter sphaeroides.

Authors:  C Benning; C R Somerville
Journal:  J Bacteriol       Date:  1992-10       Impact factor: 3.490

Review 6.  Assessment of protein coding measures.

Authors:  J W Fickett; C S Tung
Journal:  Nucleic Acids Res       Date:  1992-12-25       Impact factor: 16.971

7.  Computer prediction of the exon-intron structure of mammalian pre-mRNAs.

Authors:  M S Gelfand
Journal:  Nucleic Acids Res       Date:  1990-10-11       Impact factor: 16.971

8.  Rhodobacter capsulatus genes involved in early steps of the bacteriochlorophyll biosynthetic pathway.

Authors:  Z M Yang; C E Bauer
Journal:  J Bacteriol       Date:  1990-09       Impact factor: 3.490

9.  Subcloning, nucleotide sequence, and expression of trkG, a gene that encodes an integral membrane protein involved in potassium uptake via the Trk system of Escherichia coli.

Authors:  A Schlösser; S Kluttig; A Hamann; E P Bakker
Journal:  J Bacteriol       Date:  1991-05       Impact factor: 3.490

10.  Nucleotide sequence of an Escherichia coli chromosomal hemolysin.

Authors:  T Felmlee; S Pellett; R A Welch
Journal:  J Bacteriol       Date:  1985-07       Impact factor: 3.490
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