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Literature DB >> 8041759

Atypical regions in large genomic DNA sequences.

Abstract

Large genomic DNA sequences contain regions with distinctive patterns of sequence organization. We describe a method using logarithms of probabilities based on seventh-order Markov chains to rapidly identify genomic sequences that do not resemble models of genome organization built from compilations of octanucleotide usage. Data bases have been constructed from Escherichia coli and Saccharomyces cerevisiae DNA sequences of > 1000 nt and human sequences of > 10,000 nt. Atypical genes and clusters of genes have been located in bacteriophage, yeast, and primate DNA sequences. We consider criteria for statistical significance of the results, offer possible explanations for the observed variation in genome organization, and give additional applications of these methods in DNA sequence analysis.

Entities: Chemical Species

Mesh：

Substances：
Globins
DNA

Year: 1994 PMID： 8041759 PMCID： PMC44353 DOI： 10.1073/pnas.91.15.7134

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

17 in total

1. Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid.

Authors: J JOSSE; A D KAISER; A KORNBERG
Journal: J Biol Chem Date: 1961-03 Impact factor: 5.157

Atypical regions in large genomic DNA sequences.

1. Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid.

2. Chance and statistical significance in protein and DNA sequence analysis.

3. Corruption of genomic databases with anomalous sequence.

4. WORDUP: an efficient algorithm for discovering statistically significant patterns in DNA sequences.

5. The complete DNA sequence of yeast chromosome III.

6. The entD gene of the Escherichia coli K12 enterobactin gene cluster.

7. A bacterial virulence determinant encoded by lysogenic coliphage lambda.

8. Sequencing of chromosome I from Saccharomyces cerevisiae: analysis of a 32 kb region between the LTE1 and SPO7 genes.

Review 9. Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters.

10. Over- and under-representation of short oligonucleotides in DNA sequences.

1. Self-identification of protein-coding regions in microbial genomes.

2. Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus.

3. Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli.

4. Community-wide analysis of microbial genome sequence signatures.