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Literature DB >> 6577449

New approaches for computer analysis of nucleic acid sequences.

S Karlin, G Ghandour, F Ost, S Tavare, L J Korn.

Abstract

A new high-speed computer algorithm is outlined that ascertains within and between nucleic acid and protein sequences all direct repeats, dyad symmetries, and other structural relationships. Large repeats, repeats of high frequency, dyad symmetries of specified stem length and loop distance, and their distributions are determined. Significance of homologies is assessed by a hierarchy of permutation procedures. Applications are made to papovaviruses, the human papillomavirus HPV, lambda phage, the human and mouse mitochondrial genomes, and the human and mouse immunoglobulin kappa-chain genes.

Entities: Disease Species

Mesh：

Substances：
DNA, Viral
DNA

Year: 1983 PMID： 6577449 PMCID： PMC384318 DOI： 10.1073/pnas.80.18.5660

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

19 in total

1. Nucleotide sequence of the Hind-C fragment of simian virus 40 DNA. Comparison of the 5'-untranslated region of wild-type virus and of some deletion Mutants.

Authors: H Van Heuverswyn; W Fiers
Journal: Eur J Biochem Date: 1979-10

2. The genome of human papovavirus BKV.

Authors: I Seif; G Khoury; R Dhar
Journal: Cell Date: 1979-12 Impact factor: 41.582

3. Computer analysis of nucleic acid regulatory sequences.

Authors: L J Korn; C L Queen; M N Wegman
Journal: Proc Natl Acad Sci U S A Date: 1977-10 Impact factor: 11.205

4. Steps toward computer analysis of nucleotide sequences.

Authors: T R Gingeras; R J Roberts
Journal: Science Date: 1980-09-19 Impact factor: 47.728

5. Coding potential and regulatory signals of the polyoma virus genome.

Authors: E Soeda; J R Arrand; N Smolar; J E Walsh; B E Griffin
Journal: Nature Date: 1980-01-31 Impact factor: 49.962

6. Sequence and organization of the human mitochondrial genome.

Authors: S Anderson; A T Bankier; B G Barrell; M H de Bruijn; A R Coulson; J Drouin; I C Eperon; D P Nierlich; B A Roe; F Sanger; P H Schreier; A J Smith; R Staden; I G Young
Journal: Nature Date: 1981-04-09 Impact factor: 49.962

7. Identification of common molecular subsequences.

Authors: T F Smith; M S Waterman
Journal: J Mol Biol Date: 1981-03-25 Impact factor: 5.469

8. A computer program to search for tRNA genes.

Authors: R Staden
Journal: Nucleic Acids Res Date: 1980-02-25 Impact factor: 16.971

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. Evolution of human immunoglobulin kappa J region genes.

Authors: P A Hieter; J V Maizel; P Leder
Journal: J Biol Chem Date: 1982-02-10 Impact factor: 5.157

19 in total

1. An accurate approximation to the distribution of the length of the longest matching word between two random DNA sequences.

Authors: R F Mott; T B Kirkwood; R N Curnow
Journal: Bull Math Biol Date: 1990 Impact factor: 1.758

New approaches for computer analysis of nucleic acid sequences.

1. Nucleotide sequence of the Hind-C fragment of simian virus 40 DNA. Comparison of the 5'-untranslated region of wild-type virus and of some deletion Mutants.

2. The genome of human papovavirus BKV.

3. Computer analysis of nucleic acid regulatory sequences.

4. Steps toward computer analysis of nucleotide sequences.

5. Coding potential and regulatory signals of the polyoma virus genome.

6. Sequence and organization of the human mitochondrial genome.

7. Identification of common molecular subsequences.

8. A computer program to search for tRNA genes.

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

10. Evolution of human immunoglobulin kappa J region genes.

1. An accurate approximation to the distribution of the length of the longest matching word between two random DNA sequences.

2. A survey of multiple sequence comparison methods.

3. Poisson, compound Poisson and process approximations for testing statistical significance in sequence comparisons.

4. A source of small repeats in genomic DNA.

5. An efficient algorithm for identifying matches with errors in multiple long molecular sequences.

6. K-tuple frequency in the human genome and polymerase chain reaction.

7. Palindromic sequences are associated with sites of DNA breakage during gene conversion.

8. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.

9. Multisequence comparisons in protein coding genes. Search for functional constraints.

10. Phase transitions in sequence matches and nucleic acid structure.