Non-B DB v2.0: A database of predicted non-B DNA-forming motifs and its associated tools

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

Research output: Contribution to journalArticlepeer-review

52 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)D94-D100
JournalNucleic acids research
Volume41
Issue numberD1
DOIs
StatePublished - Jan 1 2013

Bibliographical note

Funding Information:
Funding for open access charge: This work was supported in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. HHSN261200800001E and funding from CBIIT/caBIG ISRCE yellow task #09-260 to NCI-Frederick.

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