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GBshape specifications

Information


Unique identifier OMICS_06030
Name GBshape
Alternative name Genome Browser for DNA shape annotations
Restrictions to use None
Maintained Yes

Publication for Genome Browser for DNA shape annotations

GBshape citations

 (4)
library_books

NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells

2018
PLoS One
PMCID: 5873942
PMID: 29590119
DOI: 10.1371/journal.pone.0193126

[…] oordinates of active promoters, inactive promoters, active enhancers, and poised enhancers in the human genome assembly 19 (hg19) were retrieved from the UCSC Table Browser (http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables), based on Chromatin state discovery and characterization (ChromHMM) annotation from ENCODE/Broad Institute using ENCODE ChIP-seq data for nine histone modifications in K562 c […]

library_books

Comparison of discriminative motif optimization using matrix and DNA shape based models

2018
BMC Bioinformatics
PMCID: 5840810
PMID: 29510689
DOI: 10.1186/s12859-018-2104-7

[…] itions [–]. DNAshape is a program that predicts DNA structural features in a high-throughput manner based on Monte Carlo simulations of DNA fragments []. The Genome Browser for DNA shape annotations (GBshape), a database based on DNAshape and related computational tools, provides DNA shape feature predictions for a range of organisms []. Those resources were used in a recent study where motif mode […]

library_books

Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein induced DNA deformations

2018
Nucleic Acids Res
PMCID: 5946862
PMID: 29390080
DOI: 10.1093/nar/gky033

[…] to provide an approximate map of the variation of minor groove width in DNA sequences of any length. Indeed, compORChID2 patterns for a large number of genomes (including human) are available in the GBshape database ().An interesting point in our comparison of the experimental and computed ORChID2 patterns is that the only major discrepancy appears in the long alternating pyrimidine-purine sequen […]

library_books

Mitochondrial DNA exhibits resistance to induced point and deletion mutations

2016
Nucleic Acids Res
PMCID: 5062989
PMID: 27550180
DOI: 10.1093/nar/gkw716

[…] (especially within nuclear mitochondrial segments, NUMTs, which are transpositions of mtDNA into the nucleus), and their specificity was confirmed using UCSC in silico PCR (http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgPcr) and NCBI primer-BLAST (). Additionally, melt peak analysis was performed in real-time PCR experiments along with agarose gel separation of PCR products to ensure single product […]

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GBshape institution(s)
Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA

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