TY - JOUR
T1 - Non-B DB v2.0
T2 - A database of predicted non-B DNA-forming motifs and its associated tools
AU - Cer, Regina Z.
AU - Donohue, Duncan E.
AU - Mudunuri, Uma S.
AU - Temiz, Nuri A.
AU - Loss, Michael A.
AU - Starner, Nathan J.
AU - Halusa, Goran N.
AU - Volfovsky, Natalia
AU - Yi, Ming
AU - Luke, Brian T.
AU - Bacolla, Albino
AU - Collins, Jack R.
AU - Stephens, Robert M.
N1 - 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.
PY - 2013/1/1
Y1 - 2013/1/1
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.
AB - 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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U2 - 10.1093/nar/gks955
DO - 10.1093/nar/gks955
M3 - Article
C2 - 23125372
AN - SCOPUS:84876573062
SN - 0305-1048
VL - 41
SP - D94-D100
JO - Nucleic acids research
JF - Nucleic acids research
IS - D1
ER -