Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Promoter classifier: software package for promoter database analysis.

Naum I Gershenzon1, Ilya P Ioshikhes

  • 1Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.

Applied Bioinformatics
|October 20, 2005
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Assessing the potential of quantitative 2D HSQC NMR in <sup>13</sup>C enriched living organisms.

Journal of biomolecular NMR·2019
Same author

Next-generation heteronuclear decoupling for high-field biomolecular NMR spectroscopy.

Angewandte Chemie (International ed. in English)·2014
Same author

Optimized position weight matrices in prediction of novel putative binding sites for transcription factors in the Drosophila melanogaster genome.

PloS one·2013
Same author

The Fantastic Four: A plug 'n' play set of optimal control pulses for enhancing NMR spectroscopy.

Journal of magnetic resonance (San Diego, Calif. : 1997)·2013
Same author

Optimal control design of band-selective excitation pulses that accommodate relaxation and RF inhomogeneity.

Journal of magnetic resonance (San Diego, Calif. : 1997)·2012
Same author

New strategies for designing robust universal rotation pulses: application to broadband refocusing at low power.

Journal of magnetic resonance (San Diego, Calif. : 1997)·2012
Same journal

Statistically consistent identification of differentially expressed genes in DNA chip data over the whole expression range: relative variance method.

Applied bioinformatics·2006
Same journal

A nonparametric likelihood ratio test to identify differentially expressed genes from microarray data.

Applied bioinformatics·2006
Same journal

Simulation study of ratio calculation formulae of two-colour cDNA microarray data.

Applied bioinformatics·2006
Same journal

Alternative mRNA polyadenylation can potentially affect detection of gene expression by affymetrix genechip arrays.

Applied bioinformatics·2006
Same journal

Comparisons of annotation predictions for affymetrix GeneChips.

Applied bioinformatics·2006
Same journal

Ontology annotation treebrowser : an interactive tool where the complementarity of medical subject headings and gene ontology improves the interpretation of gene lists.

Applied bioinformatics·2006
See all related articles

Promoter Classifier offers C++ programs for analyzing eukaryotic promoter sequences. This tool aids in calculating nucleotide distributions, transcription factor binding, and identifying CpG islands for large datasets.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Eukaryotic promoter sequence analysis is crucial for understanding gene regulation.
  • Handling and analyzing large datasets of promoter sequences presents computational challenges.

Purpose of the Study:

  • To introduce Promoter Classifier, a software package designed for comprehensive analysis of eukaryotic promoter sequences.
  • To provide tools for basic yet essential manipulations required for large-scale promoter dataset analysis.

Main Methods:

  • Development of seven stand-alone Windows-based C++ programs.
  • Implementation of functions for nucleotide positional distributions and transcription factor binding site analysis.
  • Inclusion of tools for subsetting sequences based on promoter elements and CpG islands, and calculating DNA biophysical properties.

Related Experiment Videos

Main Results:

  • The Promoter Classifier package enables calculation of averaged nucleotide distributions and transcription factor binding site frequencies.
  • It facilitates the division of promoter datasets into subsets based on specific elements or CpG island presence.
  • The software provides graphical outputs for DNA stacking energy and bending stiffness distributions.

Conclusions:

  • Promoter Classifier is an effective, user-friendly tool for essential manipulations of eukaryotic promoter sequences.
  • The package supports the analysis of large promoter datasets, aiding in genomic research.
  • Individual programs, like Promoter Divider, offer specialized functionalities within the package.