Literature DB >> 3839071

A method to locate protein coding sequences in DNA of prokaryotic systems.

A S Kolaskar, B V Reddy.   

Abstract

cDNA sequence data from E. coli phages, for which complete genome sequences are known, have been analysed, From this analysis thirteen triplets have been identified as markers to distinguish protein-coding frames from fortuitous open reading frames. The region of -18 to +18 nucleotides around ATG/GTG, has been analysed and used to identify initiator codons from internal ATG/GTG. With the aid of criteria defined above a method has been developed to locate protein coding sequences by a combination of 'gene search by signal' and 'gene search by content' approaches. Application of this method to prokaryotic systems including those which were not part of our data base indicates that it is quite accurate and general in nature.

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Year:  1985        PMID： 3839071      PMCID： PMC340983          DOI： 10.1093/nar/13.1.185

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


  14 in total

1.  Is UAA or UGA part of the recognition signal for ribosomal initiation?

Authors:  J F Atkins
Journal:  Nucleic Acids Res       Date:  1979-10-25       Impact factor: 16.971

Review 2.  Translational initiation in prokaryotes.

Authors:  L Gold; D Pribnow; T Schneider; S Shinedling; B S Singer; G Stormo
Journal:  Annu Rev Microbiol       Date:  1981       Impact factor: 15.500

3.  Computer methods to locate signals in nucleic acid sequences.

Authors:  R Staden
Journal:  Nucleic Acids Res       Date:  1984-01-11       Impact factor: 16.971

4.  DNA binding spectrum of the carcinogen N-acetoxy-N-2-acetylaminofluorene significantly differs from the mutation spectrum.

Authors:  R P Fuchs
Journal:  J Mol Biol       Date:  1984-07-25       Impact factor: 5.469

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

Authors:  R Staden; A D McLachlan
Journal:  Nucleic Acids Res       Date:  1982-01-11       Impact factor: 16.971

6.  The ribosome binding sites recognized by E. coli ribosomes have regions with signal character in both the leader and protein coding segments.

Authors:  G F Scherer; M D Walkinshaw; S Arnott; D J Morré
Journal:  Nucleic Acids Res       Date:  1980-09-11       Impact factor: 16.971

7.  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

8.  Recognition of protein coding regions in DNA sequences.

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

9.  A Markov analysis of DNA sequences.

Authors:  H Almagor
Journal:  J Theor Biol       Date:  1983-10-21       Impact factor: 2.691

10.  The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.

Authors:  J Shine; L Dalgarno
Journal:  Proc Natl Acad Sci U S A       Date:  1974-04       Impact factor: 11.205
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  15 in total

Review 1.  Assessment of protein coding measures.

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

2.  Characterization of two genes, glpQ and ugpQ, encoding glycerophosphoryl diester phosphodiesterases of Escherichia coli.

Authors:  J Tommassen; K Eiglmeier; S T Cole; P Overduin; T J Larson; W Boos
Journal:  Mol Gen Genet       Date:  1991-04

3.  More than 150 nucleotides flanking the initiation codon contribute to the efficiency of the ribosomal binding site from bacteriophage T7 gene 1.

Authors:  R M Geisen; H P Fatscher; E Fuchs
Journal:  Nucleic Acids Res       Date:  1987-06-25       Impact factor: 16.971

4.  Function of neisserial outer membrane phospholipase a in autolysis and assessment of its vaccine potential.

Authors:  Martine P Bos; Boris Tefsen; Pierre Voet; Vincent Weynants; Jos P M van Putten; Jan Tommassen
Journal:  Infect Immun       Date:  2005-04       Impact factor: 3.441

5.  Cloning and sequencing of IS1086, an Alcaligenes eutrophus insertion element related to IS30 and IS4351.

Authors:  Q Dong; A Sadouk; D van der Lelie; S Taghavi; A Ferhat; J M Nuyten; B Borremans; M Mergeay; A Toussaint
Journal:  J Bacteriol       Date:  1992-12       Impact factor: 3.490

6.  Transfer functions of the conjugative integrating element pSAM2 from Streptomyces ambofaciens: characterization of a kil-kor system associated with transfer.

Authors:  J Hagège; J L Pernodet; G Sezonov; C Gerbaud; A Friedmann; M Guérineau
Journal:  J Bacteriol       Date:  1993-09       Impact factor: 3.490

7.  Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases.

Authors:  E L Neidle; C Hartnett; L N Ornston; A Bairoch; M Rekik; S Harayama
Journal:  J Bacteriol       Date:  1991-09       Impact factor: 3.490

8.  Rhodobacter sphaeroides rdxA, a homolog of Rhizobium meliloti fixG, encodes a membrane protein which may bind cytoplasmic [4Fe-4S] clusters.

Authors:  E L Neidle; S Kaplan
Journal:  J Bacteriol       Date:  1992-10       Impact factor: 3.490

9.  Protein secretion in gram-negative bacteria: transport across the outer membrane involves common mechanisms in different bacteria.

Authors:  A Filloux; M Bally; G Ball; M Akrim; J Tommassen; A Lazdunski
Journal:  EMBO J       Date:  1990-12       Impact factor: 11.598

10.  Genetic rearrangement associated with in vivo mucoid conversion of Pseudomonas aeruginosa PAO is due to insertion elements.

Authors:  P A Sokol; M Z Luan; D G Storey; P Thirukkumaran
Journal:  J Bacteriol       Date:  1994-02       Impact factor: 3.476
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