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Literature DB >> 25665661

Maximum-likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores.

Abstract

A method is described for estimating the distribution and hence testing the statistical significance of sequence similarity scores obtained during a data-bank search. Maximum-likelihood is used to fit a model to the scores, avoiding any costly simulation of random sequences. The method is applied in detail to the Smith-Waterman algorithm when gaps are allowed, and is shown to give results very similar to those obtained by simulation.

Mesh：

Substances：
Proteins

Year: 1992 PMID： 25665661 DOI： 10.1007/BF02458620

Source DB: PubMed Journal: Bull Math Biol ISSN： 0092-8240 Impact factor: 1.758

13 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

2. Protein database searches for multiple alignments.

Authors: S F Altschul; D J Lipman
Journal: Proc Natl Acad Sci U S A Date: 1990-07 Impact factor: 11.205

3. Construction of validated, non-redundant composite protein sequence databases.

Authors: A J Bleasby; J C Wootton
Journal: Protein Eng Date: 1990-01

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

Authors: S Karlin; S F Altschul
Journal: Proc Natl Acad Sci U S A Date: 1990-03 Impact factor: 11.205

5. A test for the statistical significance of DNA sequence similarities for application in databank searches.

Authors: R F Mott; T B Kirkwood; R N Curnow
Journal: Comput Appl Biosci Date: 1989-04

6. Improved tools for biological sequence comparison.

Authors: W R Pearson; D J Lipman
Journal: Proc Natl Acad Sci U S A Date: 1988-04 Impact factor: 11.205

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

Authors: M S Waterman; L Gordon; R Arratia
Journal: Proc Natl Acad Sci U S A Date: 1987-03 Impact factor: 11.205

8. The significance of protein sequence similarities.

Authors: J F Collins; A F Coulson; A Lyall
Journal: Comput Appl Biosci Date: 1988-03

9. A comprehensive set of sequence analysis programs for the VAX.

Authors: J Devereux; P Haeberli; O Smithies
Journal: Nucleic Acids Res Date: 1984-01-11 Impact factor: 16.971

10. 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

18 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

Maximum-likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores.

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

2. Protein database searches for multiple alignments.

3. Construction of validated, non-redundant composite protein sequence databases.

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

5. A test for the statistical significance of DNA sequence similarities for application in databank searches.

6. Improved tools for biological sequence comparison.

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

8. The significance of protein sequence similarities.

9. A comprehensive set of sequence analysis programs for the VAX.

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

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.

3. Sensitivity and selectivity in protein structure comparison.

Review 4. The limits of protein sequence comparison?

5. A protein alignment scoring system sensitive at all evolutionary distances.

6. Finding Protein and Nucleotide Similarities with FASTA.

7. Pairwise Heuristic Sequence Alignment Algorithm Based on Deep Reinforcement Learning.

8. Local Alignment of DNA Sequence Based on Deep Reinforcement Learning.

9. New finite-size correction for local alignment score distributions.

10. Island method for estimating the statistical significance of profile-profile alignment scores.