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

doi:10.1093/nar/gks955

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 journal › Article › peer-review

161 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 language	English (US)
Pages (from-to)	D94-D100
Journal	Nucleic acids research
Volume	41
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gks955
State	Published - 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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10.1093/nar/gks955

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

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.",

author = "Cer, \{Regina Z.\} and Donohue, \{Duncan E.\} and Mudunuri, \{Uma S.\} and Temiz, \{Nuri A.\} and Loss, \{Michael A.\} and Starner, \{Nathan J.\} and Halusa, \{Goran N.\} and Natalia Volfovsky and Ming Yi and Luke, \{Brian T.\} and Albino Bacolla and Collins, \{Jack R.\} and Stephens, \{Robert M.\}",

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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doi = "10.1093/nar/gks955",

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AU - Yi, Ming

AU - Luke, Brian T.

AU - Bacolla, Albino

AU - Collins, Jack R.

AU - Stephens, Robert M.

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PY - 2013/1/1

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N2 - 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.

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

Abstract

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