Literature DB >> 6546421

Signal search analysis: a new method to localize and characterize functionally important DNA sequences.

P Bucher, B Bryan.   

Abstract

The generation of "signal search data" represents a general method of describing the common properties of a set of DNA sequences presumed to be functionally analogous. Besides the detailed description of this method we present two computer programs which use signal search data as input data: One that processes them to a "constraint profile" and another one which lists over-represented "signals" of potential functional relevance. To illustrate the possibilities of our method we have analysed a set of transcription initiation sites of sea urchin histone genes.

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Year:  1984        PMID： 6546421      PMCID： PMC321005          DOI： 10.1093/nar/12.1part1.287

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


  10 in total

1.  Integration of eukaryotic genes for 5S RNA and histone proteins into a phage lambda receptor.

Authors:  S G Clarkson; H O Smith; W Schaffner; K W Gross; M L Birnstiel
Journal:  Nucleic Acids Res       Date:  1976-10       Impact factor: 16.971

2.  Isolation of histone genes from unfractionated sea urchin DNA by subculture cloning in E. coli.

Authors:  L H Kedes; A C Chang; D Houseman; S N Cohen
Journal:  Nature       Date:  1975-06-12       Impact factor: 49.962

3.  Characterization of translational initiation sites in E. coli.

Authors:  G D Stormo; T D Schneider; L M Gold
Journal:  Nucleic Acids Res       Date:  1982-05-11       Impact factor: 16.971

4.  Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.

Authors:  G D Stormo; T D Schneider; L Gold; A Ehrenfeucht
Journal:  Nucleic Acids Res       Date:  1982-05-11       Impact factor: 16.971

5.  Comparative analysis of nucleic acid sequences by their general constraints.

Authors:  D J Lipman; J Maizel
Journal:  Nucleic Acids Res       Date:  1982-04-24       Impact factor: 16.971

6.  Identification of regulatory sequences in the prelude sequences of an H2A histone gene by the study of specific deletion mutants in vivo.

Authors:  R Grosschedl; M L Birnstiel
Journal:  Proc Natl Acad Sci U S A       Date:  1980-03       Impact factor: 11.205

7.  Sea urchin histone mRNA termini are located in gene regions downstream from putative regulatory sequences.

Authors:  C Hentschel; J C Irminger; P Bucher; M L Birnstiel
Journal:  Nature       Date:  1980-05-15       Impact factor: 49.962

8.  Ubiquitous and gene-specific regulatory 5' sequences in a sea urchin histone DNA clone coding for histone protein variants.

Authors:  M Busslinger; R Portmann; J C Irminger; M L Birnstiel
Journal:  Nucleic Acids Res       Date:  1980-03-11       Impact factor: 16.971

9.  Leader sequences of Strongylocentrotus purpuratus histone mRNAs start at a unique heptanucleotide common to all five histone genes.

Authors:  I Sures; S Levy; L H Kedes
Journal:  Proc Natl Acad Sci U S A       Date:  1980-03       Impact factor: 11.205

10.  An unusual evolutionary behaviour of a sea urchin histone gene cluster.

Authors:  M Busslinger; S Rusconi; M L Birnstiel
Journal:  EMBO J       Date:  1982       Impact factor: 11.598
  10 in total
  10 in total

1.  Signal search analysis server.

Authors:  Giovanna Ambrosini; Viviane Praz; Vidhya Jagannathan; Philipp Bucher
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

Review 2.  Databases, models, and algorithms for functional genomics: a bioinformatics perspective.

Authors:  Gautam B Singh; Harkirat Singh
Journal:  Mol Biotechnol       Date:  2005-02       Impact factor: 2.695

3.  WORDUP: an efficient algorithm for discovering statistically significant patterns in DNA sequences.

Authors:  G Pesole; N Prunella; S Liuni; M Attimonelli; C Saccone
Journal:  Nucleic Acids Res       Date:  1992-06-11       Impact factor: 16.971

4.  SQUIRREL: Sequence QUery, Information Retrieval and REporting Library. A program package for analyzing signals in nucleic acid sequences for the VAX.

Authors:  C J Gartmann; U Grob
Journal:  Nucleic Acids Res       Date:  1991-11-11       Impact factor: 16.971

5.  The Eukaryotic Promoter Database EPD.

Authors:  R Cavin Périer; T Junier; P Bucher
Journal:  Nucleic Acids Res       Date:  1998-01-01       Impact factor: 16.971

6.  Heuristic informational analysis of sequences.

Authors:  J M Claverie; L Bougueleret
Journal:  Nucleic Acids Res       Date:  1986-01-10       Impact factor: 16.971

7.  Compilation and analysis of eukaryotic POL II promoter sequences.

Authors:  P Bucher; E N Trifonov
Journal:  Nucleic Acids Res       Date:  1986-12-22       Impact factor: 16.971

8.  Discrimination of phytochrome dependent light inducible from non-light inducible plant genes. Prediction of a common light-responsive element (LRE) in phytochrome dependent light inducible plant genes.

Authors:  U Grob; K Stüber
Journal:  Nucleic Acids Res       Date:  1987-12-10       Impact factor: 16.971

9.  Identifying putative promoter regions of Hermansky-Pudlak syndrome genes by means of phylogenetic footprinting.

Authors:  Horia Stanescu; Tyra G Wolfsberg; R Travis Moreland; Mariam H Ayub; Elizabeth Erickson; Wendy Westbroek; Marjan Huizing; William A Gahl; Amanda Helip-Wooley
Journal:  Ann Hum Genet       Date:  2009-07       Impact factor: 1.670

10.  The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

Authors:  Giovanna Ambrosini; René Dreos; Sunil Kumar; Philipp Bucher
Journal:  BMC Genomics       Date:  2016-11-18       Impact factor: 3.969
  10 in total

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