A search for patterns in the nucleotide sequence of the MS2 genome

  title={A search for patterns in the nucleotide sequence of the MS2 genome},
  author={John W. Erickson and Gary George Altman},
  journal={Journal of Mathematical Biology},
SummaryThe nucleotide sequence of the RNA of the bacteriophage MS2 was examined by computer for internal patterns. We used a technique which analyzes a nucleotide sequence as a Markov chain. This led us to discover patterns within the translated and untranslated regions of the RNA in addition to those patterns formed by the codons. One of the more surprising results of this analysis was the discovery that the non-coding sequences in the genome are as highly ordered, although in a different… Expand
Statistical Predictions of Coding Regions in Prokaryotic Genomes by Using Inhomogeneous Markov Models
The chapter talks about higher-order models and models of typical and atypical genes, a category of special interest for evolutionary studies, as well as for studies of pathogenic bacteria whose pathogenicity islands or antibiotic-resistance genes could be relatively recent additions to the whole genome. Expand
A thermodynamic theory of codon bias in viral genes.
Using a four-state Ising-like model with stacking interactions between successive base pairs, it is shown how primeval periodic DNA polymers could have arisen the remnants of which are still observed in codon biases today. Expand
On the informational content of viral DNA.
The general problem of defining information content is discussed and a procedure for analysis extended from that of Gatlin (1972) is developed and long range correlations in base sequences are analyzed for several viral genomes. Expand
Codon preference and primary sequence structure in protein-coding regions.
The stochastic complexity of a data base of 365 protein-coding regions is analysed and the fit to observed codon preference is very poor when the primary sequence is modeled as a spatially homogeneous Markov source, but improves substantially when a non-homogeneous model is used. Expand
Methyltransferases as tools to alter the specificity of restriction endonucleases.
This chapter describes enzymatic strategies to generate large DNA fragments and statistical tools that can aid researchers in choosing the restriction enzymes that are most likely to generated large fragments in the genome in question, if a sequence data base can be investigated. Expand
Between a chicken and a grape: estimating the number of human genes
Ever since the discovery of the genetic code, scientists have been trying to catalog all the genes in the human genome. Over the years, the best estimate of the number of human genes has grownExpand
Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eucaryotic nuclear DNA sequences both protein-coding and noncoding
  • B. Blaisdell
  • Biology, Medicine
  • Journal of Molecular Evolution
  • 2005
A considerable sample of eucaryotic nuclear DNA sequences have significant local structure over subsequences of three to five contiguous bases, and that this structure occurs throughout the total length of the sequence. Expand
Physical Mapping and Fingerprinting of Bacterial Genomes using Rare Cutting Restriction Enzymes
Pulsed-field gel electrophoresis (PFGE) has allowed the separation of DNA fragments of five million base pairs or more, which is about the same size or greater than most bacterial genomes. When aExpand
Context-Dependent Evolutionary Models for Non-Coding Sequences: An Overview of Several Decades of Research and an Analysis of Laurasiatheria and Primate Evolution
This paper discusses various approaches presented in recent years to model context-dependent evolution, and presents new results on two mammalian datasets to shed a light on so-called lineage-dependent context- dependent evolution. Expand
A bibliography on computational molecular biology and genetics
The field of computational molecular biology and genetics is expanding at an enormous rate. Journals such as CABIOS and Nucleic Acids Research routinely publish articles on computational andExpand


Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene
The complete, primary chemical structure of a viral genome has now been established and biological properties, such as ribosome binding and codon interactions can now be discussed on a molecular basis. Expand
Nucleotide Sequence of the Gene Coding for the Bacteriophage MS2 Coat Protein
By characterization of fragments, isolated from a nuclease digest of MS2 RNA, the entire nucleotide sequence of the coat gene was established. A “flower”-like model is proposed for the secondaryExpand
Studies on the bacteriophages MS2. XXXIII. Comparison of the nucleotide sequences in related bacteriophage RNAs.
There is clearly a selective pressure to preserve at least certain aspects of the three-dimensional conformation of the MS2 bacteriophage RNA sequence, as the amount of variation in double-stranded regions is much lower than the relative degree of secondary structure of the RNA would predict. Expand
Nucleotide sequence of bacteriophage φX174 DNA
The sequence identifies many of the features responsible for the production of the proteins of the nine known genes of the organism, including initiation and termination sites for the proteins and RNAs. Expand
A test for nucleotide sequence homology.
A test is developed which computes the significance of each deletion/insertion hypothesized, based on Monte-Carlo sampling of random sequences with the same base composition as the experimental sequences being tested, which confirms the relation of Escherichia coli and KB carcinoma 5 S RNAs and establishes the previously undetected homology between Pseudomonas fluorescens and KB 5 SRNAs. Expand
Sequence homologies between ribosomal and phage RNAs: a proposed molecular basis for RNA phage parasitism.
Abstract An extensive nucleotide sequence homology between the 3′-end of the 16 S ribosomal RNA and segments of bacteriophage MS2 or Qβ RNA is described. In addition, a notable sequence homology ofExpand
Studies on the bacteriophage MS2 6. The nucleoside 5'-triphosphate end groups of the replicative intermediate and the replicative form.
The viral proteins synthesized in non-suppressor cells by amber mutants in the A protein cistron of the RNA bacteriophage MS2 were analyzed and it was shown that the absence of fragment is not due to selective proteolytic breakdown. Expand
A-Protein gene of bacteriophage MS2
The nucleotide sequence of the A-protein gene of bacteriophage MS2 has been determined and a model for its secondary structure is proposed. Also the amino acid sequence of the A-protein has beenExpand
3'-Terminal nucletide sequence (n equals 361) of bacteriophage MS2 RNA.
32P-Labeled MS2 RNA was partially digested with ribonuclease T1 and a unique reading frame could be deduced, which indicated that the replicase gene ends with a U-A-G termination signal and is followed by a 174-nucleotide-long untranslated segment. Expand
Tests for Contingency Tables and Marltov Chains
A number of useful tests for contingency tables and finite stationary Markov chains are presented in this paper based on the use of the notions of information theory. A consistent and simple approachExpand