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Literature DB >> 2994049

Comparative statistics for DNA and protein sequences: single sequence analysis.

Abstract

Four categories of data representations are used to help interpret structures and similarities of nucleic acid and protein sequences. Statistical significance of the observed relationships revealed by these representations are assessed by a hierarchy of permutation procedures and by comparisons with theoretical random models. Applications are presented for various DNA sequences including papovaviruses, Epstein-Barr virus, mitochondrial genomes, and several globin and immunoglobulin genes.

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Year: 1985 PMID： 2994049 PMCID： PMC390640 DOI： 10.1073/pnas.82.17.5800

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

10 in total

1. DNA sequence and expression of the B95-8 Epstein-Barr virus genome.

Authors: R Baer; A T Bankier; M D Biggin; P L Deininger; P J Farrell; T J Gibson; G Hatfull; G S Hudson; S C Satchwell; C Séguin
Journal: Nature Date: 1984 Jul 19-25 Impact factor: 49.962

2. Unusual regulation of simian virus 40 early-region transcription in genomes containing two origins of DNA replication.

Authors: A R Buchman; P Berg
Journal: Mol Cell Biol Date: 1984-09 Impact factor: 4.272

3. Organization of the Epstein-Barr virus DNA molecule. II. Fine mapping of the boundaries of the internal repeat cluster of B95-8 and identification of additional small tandem repeats adjacent to the HR-1 deletion.

Authors: S D Hayward; S G Lazarowitz; G S Hayward
Journal: J Virol Date: 1982-07 Impact factor: 5.103

4. Statistical characterization of nucleic acid sequence functional domains.

Authors: T F Smith; M S Waterman; J R Sadler
Journal: Nucleic Acids Res Date: 1983-04-11 Impact factor: 16.971

5. Random sequences.

Authors: W M Fitch
Journal: J Mol Biol Date: 1983-01-15 Impact factor: 5.469

6. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements.

Authors: J J Dunn; F W Studier
Journal: J Mol Biol Date: 1983-06-05 Impact factor: 5.469

7. Permutation methods for the structured exploratory data analysis (SEDA) of familial trait values.

Authors: S Karlin; P T Williams
Journal: Am J Hum Genet Date: 1984-07 Impact factor: 11.025

8. Similar amino acid sequences: chance or common ancestry?

Authors: R F Doolittle
Journal: Science Date: 1981-10-09 Impact factor: 47.728

9. Translational coupling during expression of the tryptophan operon of Escherichia coli.

Authors: D S Oppenheim; C Yanofsky
Journal: Genetics Date: 1980-08 Impact factor: 4.562

10. Evidence for higher rates of nucleotide substitution in rodents than in man.

Authors: C I Wu; W H Li
Journal: Proc Natl Acad Sci U S A Date: 1985-03 Impact factor: 11.205

10 in total

11 in total

1. Corruption of genomic databases with anomalous sequence.

Authors: E D Lamperti; J M Kittelberger; T F Smith; L Villa-Komaroff
Journal: Nucleic Acids Res Date: 1992-06-11 Impact factor: 16.971

2. A model for the development of the tandem repeat units in the EBV ori-P region and a discussion of their possible function.

Authors: S Karlin; B E Blaisdell
Journal: J Mol Evol Date: 1987 Impact factor: 2.395

Comparative statistics for DNA and protein sequences: single sequence analysis.

1. DNA sequence and expression of the B95-8 Epstein-Barr virus genome.

2. Unusual regulation of simian virus 40 early-region transcription in genomes containing two origins of DNA replication.

3. Organization of the Epstein-Barr virus DNA molecule. II. Fine mapping of the boundaries of the internal repeat cluster of B95-8 and identification of additional small tandem repeats adjacent to the HR-1 deletion.

4. Statistical characterization of nucleic acid sequence functional domains.

5. Random sequences.

6. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements.

7. Permutation methods for the structured exploratory data analysis (SEDA) of familial trait values.

8. Similar amino acid sequences: chance or common ancestry?

9. Translational coupling during expression of the tryptophan operon of Escherichia coli.

10. Evidence for higher rates of nucleotide substitution in rodents than in man.

1. Corruption of genomic databases with anomalous sequence.

2. A model for the development of the tandem repeat units in the EBV ori-P region and a discussion of their possible function.

3. Significant potential secondary structures in the Epstein-Barr virus genome.

4. Comparative statistics for DNA and protein sequences: multiple sequence analysis.

5. A nonlinear measure of subalignment similarity and its significance levels.

6. DNA sequence patterns in human, mouse, and rabbit immunoglobulin kappa-genes.

Review 7. DNA turnover and the molecular clock.

8. Modular sequence elements associated with origin regions in eukaryotic chromosomal DNA.

9. Contrasts in codon usage of latent versus productive genes of Epstein-Barr virus: data and hypotheses.

10. CLUSS: clustering of protein sequences based on a new similarity measure.