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Literature DB >> 16593289

Optimal sequence alignments.

Abstract

Current theory is adequate to the task of finding an optimal alignment between two character strings such as nucleic acids. Most algorithms currently in use must fail to find the homologous alignment between a set of codons for the chicken alpha- and beta-hemoglobin sequence when it is in fact discoverable by a more general treatment of gaps. Fundamental reasons for this are discussed.

Entities: Species

Year: 1983 PMID： 16593289 PMCID： PMC393601 DOI： 10.1073/pnas.80.5.1382

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

5 in total

1. Pattern recognition in genetic sequences.

Authors: P H Sellers
Journal: Proc Natl Acad Sci U S A Date: 1979-07 Impact factor: 11.205

2. 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

3. Molecular cloning and sequence analysis of adult chicken betal globin cDNA.

Authors: R I Richards; J Shine; A Ullrich; J R Wells; H M Goodman
Journal: Nucleic Acids Res Date: 1979-11-10 Impact factor: 16.971

4. Comparative biosequence metrics.

Authors: T F Smith; M S Waterman; W M Fitch
Journal: J Mol Evol Date: 1981 Impact factor: 2.395

5. Complete nucleotide sequence of a cloned chicken alpha-globin cDNA.

Authors: N J Deacon; J Shine; H Naora
Journal: Nucleic Acids Res Date: 1980-03-25 Impact factor: 16.971

5 in total

49 in total

1. The estimation of statistical parameters for local alignment score distributions.

Authors: S F Altschul; R Bundschuh; R Olsen; T Hwa
Journal: Nucleic Acids Res Date: 2001-01-15 Impact factor: 16.971

Review 2. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Authors: A A Schäffer; L Aravind; T L Madden; S Shavirin; J L Spouge; Y I Wolf; E V Koonin; S F Altschul
Journal: Nucleic Acids Res Date: 2001-07-15 Impact factor: 16.971

Optimal sequence alignments.

1. Pattern recognition in genetic sequences.

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

3. Molecular cloning and sequence analysis of adult chicken betal globin cDNA.

4. Comparative biosequence metrics.

5. Complete nucleotide sequence of a cloned chicken alpha-globin cDNA.

1. The estimation of statistical parameters for local alignment score distributions.

Review 2. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Review 3. Inching toward reality: an improved likelihood model of sequence evolution.

4. A survey of multiple sequence comparison methods.

5. Parametric sequence comparisons.

6. Sequence alignments in the neighborhood of the optimum with general application to dynamic programming.

7. An evolutionary model for maximum likelihood alignment of DNA sequences.

8. Evidence, content and corroboration and the Tree of Life.

9. The molecular biology computer research resource.

10. A basic analysis toolkit for biological sequences.