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 journalArticle

48 Citations (Scopus)

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)
JournalNucleic acids research
Volume41
Issue numberD1
DOIs
StatePublished - Jan 1 2013

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Platypus
Pongo
Z-Form DNA
G-Quadruplexes
Nucleotide Motifs
Pan troglodytes
Nucleic Acid Repetitive Sequences
Macaca
Genomics
Arabidopsis
Microsatellite Repeats
Horses
Swine
Genome
Databases
Dogs

Cite this

Cer, R. Z., Donohue, D. E., Mudunuri, U. S., Temiz, N. A., Loss, M. A., Starner, N. J., ... Stephens, R. M. (2013). Non-B DB v2.0: A database of predicted non-B DNA-forming motifs and its associated tools. Nucleic acids research, 41(D1). https://doi.org/10.1093/nar/gks955

Non-B DB v2.0 : A database of predicted non-B DNA-forming motifs and its associated tools. / Cer, Regina Z.; Donohue, Duncan E.; Mudunuri, Uma S.; Temiz, Nuri A.; Loss, Michael A.; Starner, Nathan J.; Halusa, Goran N.; Volfovsky, Natalia; Yi, Ming; Luke, Brian T.; Bacolla, Albino; Collins, Jack R.; Stephens, Robert M.

In: Nucleic acids research, Vol. 41, No. D1, 01.01.2013.

Research output: Contribution to journalArticle

Cer, RZ, Donohue, DE, Mudunuri, US, Temiz, NA, Loss, MA, Starner, NJ, Halusa, GN, Volfovsky, N, Yi, M, Luke, BT, Bacolla, A, Collins, JR & Stephens, RM 2013, 'Non-B DB v2.0: A database of predicted non-B DNA-forming motifs and its associated tools', Nucleic acids research, vol. 41, no. D1. https://doi.org/10.1093/nar/gks955
Cer, Regina Z. ; Donohue, Duncan E. ; Mudunuri, Uma S. ; Temiz, Nuri A. ; Loss, Michael A. ; Starner, Nathan J. ; Halusa, Goran N. ; Volfovsky, Natalia ; Yi, Ming ; Luke, Brian T. ; Bacolla, Albino ; Collins, Jack R. ; Stephens, Robert M. / Non-B DB v2.0 : A database of predicted non-B DNA-forming motifs and its associated tools. In: Nucleic acids research. 2013 ; Vol. 41, No. D1.
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