Literature DB >> 1942056

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

M Y Leung1, B E Blaisdell, C Burge, S Karlin.   

Abstract

An efficient algorithm is described for finding matches, repeats and other word relations, allowing for errors, in large data sets of long molecular sequences. The algorithm entails hashing on fixed-size words in conjunction with the use of a linked list connecting all occurrences of the same word. The average memory and run time requirement both increase almost linearly with the total sequence length. Some results of the program's performance on a database of Escherichia coli DNA sequences are presented.

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Year:  1991        PMID： 1942056      PMCID： PMC4076298          DOI： 10.1016/0022-2836(91)90938-3

Source DB:  PubMed          Journal:  J Mol Biol        ISSN： 0022-2836            Impact factor:   5.469


  23 in total

1.  A workbench for multiple alignment construction and analysis.

Authors:  G D Schuler; S F Altschul; D J Lipman
Journal:  Proteins       Date:  1991

2.  Palindromic units are part of a new bacterial interspersed mosaic element (BIME).

Authors:  E Gilson; W Saurin; D Perrin; S Bachellier; M Hofnung
Journal:  Nucleic Acids Res       Date:  1991-04-11       Impact factor: 16.971

3.  Methods for discovering novel motifs in nucleic acid sequences.

Authors:  R Staden
Journal:  Comput Appl Biosci       Date:  1989-10

Review 4.  Linkage map of Escherichia coli K-12, edition 8.

Authors:  B J Bachmann
Journal:  Microbiol Rev       Date:  1990-06

5.  Identification of consensus patterns in unaligned DNA sequences known to be functionally related.

Authors:  G Z Hertz; G W Hartzell; G D Stormo
Journal:  Comput Appl Biosci       Date:  1990-04

6.  Searching through sequence databases.

Authors:  R F Doolittle
Journal:  Methods Enzymol       Date:  1990       Impact factor: 1.600

7.  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

8.  Algorithms for identifying local molecular sequence features.

Authors:  S Karlin; M Morris; G Ghandour; M Y Leung
Journal:  Comput Appl Biosci       Date:  1988-03

9.  A novel intercistronic regulatory element of prokaryotic operons.

Authors:  C F Higgins; G F Ames; W M Barnes; J M Clement; M Hofnung
Journal:  Nature       Date:  1982-08-19       Impact factor: 49.962

10.  Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map.

Authors:  K E Rudd; W Miller; J Ostell; D A Benson
Journal:  Nucleic Acids Res       Date:  1990-01-25       Impact factor: 16.971
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  14 in total

1.  Methods and algorithms for statistical analysis of protein sequences.

Authors:  V Brendel; P Bucher; I R Nourbakhsh; B E Blaisdell; S Karlin
Journal:  Proc Natl Acad Sci U S A       Date:  1992-03-15       Impact factor: 11.205

Review 2.  Nonrandom clusters of palindromes in herpesvirus genomes.

Authors:  Ming-Ying Leung; Kwok Pui Choi; Aihua Xia; Louis H Y Chen
Journal:  J Comput Biol       Date:  2005-04       Impact factor: 1.479

Review 3.  Statistical signals in bioinformatics.

Authors:  Samuel Karlin
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-12       Impact factor: 11.205

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

Authors:  G A Schachtel; P Bucher; E S Mocarski; B E Blaisdell; S Karlin
Journal:  J Mol Evol       Date:  1991-12       Impact factor: 2.395

5.  Molecular characterization of a mutable pigmentation phenotype and isolation of the first active transposable element from Sorghum bicolor.

Authors:  S Chopra; V Brendel; J Zhang; J D Axtell; T Peterson
Journal:  Proc Natl Acad Sci U S A       Date:  1999-12-21       Impact factor: 11.205

6.  Protein sequence randomness and sequence/structure correlations.

Authors:  R S Rahman; S Rackovsky
Journal:  Biophys J       Date:  1995-04       Impact factor: 4.033

7.  Assessments of DNA inhomogeneities in yeast chromosome III.

Authors:  S Karlin; B E Blaisdell; R J Sapolsky; L Cardon; C Burge
Journal:  Nucleic Acids Res       Date:  1993-02-11       Impact factor: 16.971

8.  Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria.

Authors:  G P Dimri; K E Rudd; M K Morgan; H Bayat; G F Ames
Journal:  J Bacteriol       Date:  1992-07       Impact factor: 3.490

9.  Comparative DNA sequence features in two long Escherichia coli contigs.

Authors:  L R Cardon; C Burge; G A Schachtel; B E Blaisdell; S Karlin
Journal:  Nucleic Acids Res       Date:  1993-08-11       Impact factor: 16.971

10.  Intrastrand triplex DNA repeats in bacteria: a source of genomic instability.

Authors:  Isabelle T Holder; Stefanie Wagner; Peiwen Xiong; Malte Sinn; Tancred Frickey; Axel Meyer; Jörg S Hartig
Journal:  Nucleic Acids Res       Date:  2015-10-07       Impact factor: 16.971
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