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Literature DB >> 3124111

Efficient algorithms for molecular sequence analysis.

S Karlin¹, M Morris, G Ghandour, M Y Leung.

Abstract

Efficient (linear time) algorithms are described for identifying global molecular sequence features allowing for errors including repeats, matches between sequences, dyad symmetry pairings, and other sequence patterns. A multiple sequence alignment algorithm is also described. Specific applications are given to hepatitis B viruses and the J5-C (J, joining; C, constant) region of the immunoglobulin kappa gene.

Entities: Disease

Mesh：

Substances：

Year: 1988 PMID： 3124111 PMCID： PMC279651 DOI： 10.1073/pnas.85.3.841

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

8 in total

1. A general method applicable to the search for similarities in the amino acid sequence of two proteins.

Authors: S B Needleman; C D Wunsch
Journal: J Mol Biol Date: 1970-03 Impact factor: 5.469

2. DNA sequence comparisons of the human, mouse, and rabbit immunoglobulin kappa gene.

Authors: S Karlin; G Ghandour; D E Foulser
Journal: Mol Biol Evol Date: 1985-01 Impact factor: 16.240

3. Comparative analysis of human and bovine papillomaviruses.

Authors: S Karlin; G Ghandour; D E Foulser; L J Korn
Journal: Mol Biol Evol Date: 1984-07 Impact factor: 16.240

4. Immunoglobulin gene transcription is activated by downstream sequence elements.

Authors: C Queen; D Baltimore
Journal: Cell Date: 1983-07 Impact factor: 41.582

5. A simple method for displaying the hydropathic character of a protein.

Authors: J Kyte; R F Doolittle
Journal: J Mol Biol Date: 1982-05-05 Impact factor: 5.469

6. Rapid similarity searches of nucleic acid and protein data banks.

Authors: W J Wilbur; D J Lipman
Journal: Proc Natl Acad Sci U S A Date: 1983-02 Impact factor: 11.205

7. Nucleotide sequence of an infectious molecularly cloned genome of ground squirrel hepatitis virus.

Authors: C Seeger; D Ganem; H E Varmus
Journal: J Virol Date: 1984-08 Impact factor: 5.103

8. The use of multiple alphabets in kappa-gene immunoglobulin DNA sequence comparisons.

Authors: S Karlin; G Ghandour
Journal: EMBO J Date: 1985-05 Impact factor: 11.598

8 in total

1. An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction.

Authors: Eduardo P C Rocha
Journal: Genome Res Date: 2003-05-12 Impact factor: 9.043

2. Phylogenetic continuum indicates "galaxies" in the protein universe: preliminary results on the natural group structures of proteins.

Authors: I Ladunga
Journal: J Mol Evol Date: 1992-04 Impact factor: 2.395

7. Average values of a dissimilarity measure not requiring sequence alignment are twice the averages of conventional mismatch counts requiring sequence alignment for a computer-generated model system.

Authors: B E Blaisdell
Journal: J Mol Evol Date: 1989-12 Impact factor: 2.395

8. Effectiveness of measures requiring and not requiring prior sequence alignment for estimating the dissimilarity of natural sequences.

Authors: B E Blaisdell
Journal: J Mol Evol Date: 1989-12 Impact factor: 2.395

8 in total

Efficient algorithms for molecular sequence analysis.

1. A general method applicable to the search for similarities in the amino acid sequence of two proteins.

2. DNA sequence comparisons of the human, mouse, and rabbit immunoglobulin kappa gene.

3. Comparative analysis of human and bovine papillomaviruses.

4. Immunoglobulin gene transcription is activated by downstream sequence elements.

5. A simple method for displaying the hydropathic character of a protein.

6. Rapid similarity searches of nucleic acid and protein data banks.

7. Nucleotide sequence of an infectious molecularly cloned genome of ground squirrel hepatitis virus.

8. The use of multiple alphabets in kappa-gene immunoglobulin DNA sequence comparisons.

1. An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction.

2. Phylogenetic continuum indicates "galaxies" in the protein universe: preliminary results on the natural group structures of proteins.

3. Evidence for selective evolution in codon usage in conserved amino acid segments of human alphaherpesvirus proteins.

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

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

6. Searching microsatellites in DNA sequences: approaches used and tools developed.

7. Average values of a dissimilarity measure not requiring sequence alignment are twice the averages of conventional mismatch counts requiring sequence alignment for a computer-generated model system.

8. Effectiveness of measures requiring and not requiring prior sequence alignment for estimating the dissimilarity of natural sequences.