Literature DB >> 9228617

An efficient statistic to detect over- and under-represented words in DNA sequences.

S Schbath1.   

Abstract

In this note, we point out a very efficient statistic to detect over- and under-represented words in DNA sequences, when Markov chain models are used to represent the sequences. This statistic is missing from the recent review done on this important problem and appears to be a better measure of rarity and abundance of words in DNA sequences.

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Year:  1997        PMID： 9228617     DOI： 10.1089/cmb.1997.4.189

Source DB:  PubMed          Journal:  J Comput Biol        ISSN： 1066-5277            Impact factor:   1.479


  17 in total

1.  In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species.

Authors:  J H Graber; C R Cantor; S C Mohr; T F Smith
Journal:  Proc Natl Acad Sci U S A       Date:  1999-11-23       Impact factor: 11.205

2.  SPA: Simple web tool to assess statistical significance of DNA patterns.

Authors:  H Richard; G Nuel
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

Review 3.  Computational approaches to identify promoters and cis-regulatory elements in plant genomes.

Authors:  Stephane Rombauts; Kobe Florquin; Magali Lescot; Kathleen Marchal; Pierre Rouzé; Yves van de Peer
Journal:  Plant Physiol       Date:  2003-07       Impact factor: 8.340

4.  Statistical analysis of over-represented words in human promoter sequences.

Authors:  Leonardo Mariño-Ramírez; John L Spouge; Gavin C Kanga; David Landsman
Journal:  Nucleic Acids Res       Date:  2004-02-12       Impact factor: 16.971

5.  Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation.

Authors:  Jun Hu; Carol S Lutz; Jeffrey Wilusz; Bin Tian
Journal:  RNA       Date:  2005-08-30       Impact factor: 4.942

6.  Alignments anchored on genomic landmarks can aid in the identification of regulatory elements.

Authors:  Kannan Tharakaraman; Leonardo Mariño-Ramírez; Sergey Sheetlin; David Landsman; John L Spouge
Journal:  Bioinformatics       Date:  2005-06       Impact factor: 6.937

7.  High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli.

Authors:  Ekaterina Savitskaya; Ekaterina Semenova; Vladimir Dedkov; Anastasia Metlitskaya; Konstantin Severinov
Journal:  RNA Biol       Date:  2013-04-25       Impact factor: 4.652

8.  ColorPhylo: A Color Code to Accurately Display Taxonomic Classifications.

Authors:  Sylvain Lespinats; Bernard Fertil
Journal:  Evol Bioinform Online       Date:  2011-11-13       Impact factor: 1.625

9.  Integrating overlapping structures and background information of words significantly improves biological sequence comparison.

Authors:  Qi Dai; Lihua Li; Xiaoqing Liu; Yuhua Yao; Fukun Zhao; Michael Zhang
Journal:  PLoS One       Date:  2011-11-10       Impact factor: 3.240

10.  The adaptation of temperate bacteriophages to their host genomes.

Authors:  Louis-Marie Bobay; Eduardo P C Rocha; Marie Touchon
Journal:  Mol Biol Evol       Date:  2012-12-12       Impact factor: 16.240
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