Literature DB >> 6546419

Rapid searches for complex patterns in biological molecules.

R M Abarbanel, P R Wieneke, E Mansfield, D A Jaffe, D L Brutlag.   

Abstract

The intrinsic redundancy of genetic information makes searching for patterns in biological sequences a difficult task. We have designed an interactive self-documenting computer program called QUEST that allows rapid searching of large DNA and protein data banks for highly redundant consensus sequences or character patterns. QUEST uses a concise language for specifying character patterns containing several levels of ambiguity and pattern arrangement. Examples of the use of this program for sequence data are given. Details of the algorithm and pattern optimization are explained.

Mesh：

Year:  1984        PMID： 6546419      PMCID： PMC321003          DOI： 10.1093/nar/12.1part1.263

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  2 in total

1.  Prediction of super-secondary structure in proteins.

Authors:  W R Taylor; J M Thornton
Journal:  Nature       Date:  1983-02-10       Impact factor: 49.962

2.  SEQ: a nucleotide sequence analysis and recombination system.

Authors:  D L Brutlag; J Clayton; P Friedland; L H Kedes
Journal:  Nucleic Acids Res       Date:  1982-01-11       Impact factor: 16.971
  2 in total
  10 in total

1.  Automatic generation of primary sequence patterns from sets of related protein sequences.

Authors:  R F Smith; T F Smith
Journal:  Proc Natl Acad Sci U S A       Date:  1990-01       Impact factor: 11.205

2.  Codon usage in histone gene families of higher eukaryotes reflects functional rather than phylogenetic relationships.

Authors:  D Wells; W Bains; L Kedes
Journal:  J Mol Evol       Date:  1986       Impact factor: 2.395

3.  The multiple origins of human Alu sequences.

Authors:  W Bains
Journal:  J Mol Evol       Date:  1986       Impact factor: 2.395

4.  Approximate matching of regular expressions.

Authors:  E W Myers; W Miller
Journal:  Bull Math Biol       Date:  1989       Impact factor: 1.758

5.  Stochastic context-free grammars for tRNA modeling.

Authors:  Y Sakakibara; M Brown; R Hughey; I S Mian; K Sjölander; R C Underwood; D Haussler
Journal:  Nucleic Acids Res       Date:  1994-11-25       Impact factor: 16.971

6.  Generation of expressed sequence tags of random root cDNA clones of Brassica napus by single-run partial sequencing.

Authors:  Y S Park; J M Kwak; O Y Kwon; Y S Kim; D S Lee; M J Cho; H H Lee; H G Nam
Journal:  Plant Physiol       Date:  1993-10       Impact factor: 8.340

7.  Pattern recognition in several sequences: consensus and alignment.

Authors:  M S Waterman; R Arratia; D J Galas
Journal:  Bull Math Biol       Date:  1984       Impact factor: 1.758

8.  Sixty-nine kilobases of contiguous human genomic sequence containing the alpha-galactosidase A and Bruton's tyrosine kinase loci.

Authors:  J C Oeltjen; X Liu; J Lu; R C Allen; D Muzny; J W Belmont; R A Gibbs
Journal:  Mamm Genome       Date:  1995-05       Impact factor: 2.957

9.  eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity.

Authors:  Qiaojuan Jane Su; Lin Lu; Serge Saxonov; Douglas L Brutlag
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

10.  A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli.

Authors:  E Gilson; J M Clément; D Brutlag; M Hofnung
Journal:  EMBO J       Date:  1984-06       Impact factor: 11.598
  10 in total

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