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|Alternative name||Genome Browser for DNA shape annotations|
|Restrictions to use||None|
Publication for Genome Browser for DNA shape annotations
NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells
[…] 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 […]
Comparison of discriminative motif optimization using matrix and DNA shape based models
[…] 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 […]
Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein induced DNA deformations
[…] 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 […]
Mitochondrial DNA exhibits resistance to induced point and deletion mutations
[…] (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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