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Database Commons - Non-B DB

Non-B DB

Citations: 68

z-index 0.00

Short name Non-B DB
Full name A Database for Integrated Annotations and Analysis of non-B DNA Forming Motifs
Description The non-B DB catalogs predicted non-B DNA-forming sequence motifs,including Z-DNA,G-quadruplex,A-phased repeats,inverted repeats,mirror repeats,direct repeats and their corresponding subsets
URL https://nonb-abcc.ncifcrf.gov/apps/site/default
Year founded 2010
Last update & version 2012-06-13    v2.0
Availability Free to all users
University/Institution hosted Frederick National Laboratory for Cancer Research
Address Frederick,MD 21702
City Frederick
Province/State MD
Country/Region United States
Contact name Robert M. Stephens
Contact email stephensr@mail.nih.gov
Data type(s)
Major organism(s)
Keyword(s)
  • non-B DNA-forming motif
Publication(s)
  • Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools. [PMID: 23125372]

    Regina Z Cer, Duncan E Donohue, Uma S Mudunuri, Nuri A Temiz, Michael A Loss, Nathan J Starner, Goran N Halusa, Natalia Volfovsky, Ming Yi, Brian T Luke, Albino Bacolla, Jack R Collins, Robert M Stephens
    Nucleic acids research 2013:41(Database issue)
    27 Citations (Google Scholar as of 2016-05-02)

    Abstract: The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance.

  • Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes. [PMID: 21097885]

    Regina Z Cer, Kevin H Bruce, Uma S Mudunuri, Ming Yi, Natalia Volfovsky, Brian T Luke, Albino Bacolla, Jack R Collins, Robert M Stephens
    Nucleic acids research 2011:39(Database issue)
    41 Citations (Google Scholar as of 2016-05-02)

    Abstract: Although the capability of DNA to form a variety of non-canonical (non-B) structures has long been recognized, the overall significance of these alternate conformations in biology has only recently become accepted en masse. In order to provide access to genome-wide locations of these classes of predicted structures, we have developed non-B DB, a database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides the most complete list of alternative DNA structure predictions available, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively. The database also contains motifs predicted to form static DNA bends, short tandem repeats and homo(purine‚ÄĘpyrimidine) tracts that have been associated with disease. The database has been built using the latest releases of the human, chimp, dog, macaque and mouse genomes, so that the results can be compared directly with other data sources. In order to make the data interpretable in a genomic context, features such as genes, single-nucleotide polymorphisms and repetitive elements (SINE, LINE, etc.) have also been incorporated. The database is accessed through query pages that produce results with links to the UCSC browser and a GBrowse-based genomic viewer. It is freely accessible at http://nonb.abcc.ncifcrf.gov.

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Tags

DNA
Canis familiaris Homo sapiens Mus musculus Pan troglodytes
non-B DNA-forming motif

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Zhang Zhang [2016-05-08]
    • Lin Liu [2016-03-28]
    • Li Yang [2015-11-24]
    • Li Yang [2015-06-26]
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