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Sole-Search specifications


Unique identifier OMICS_11176
Name Sole-Search
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No


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Sole-Search citations


Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network

Nucleic Acids Res
PMCID: 5737700
PMID: 28985358
DOI: 10.1093/nar/gkx672

[…] analysis on pooled reads from input and immuno-precipitated chromatins. fifty one false-positive peaks located in amplified regions of the input genome were removed of the set of called peaks using sole-search (). the remaining 4638 peaks were annotated with the three closest neighboring genes at a maximal distance of 20 kb using cisgenome. enriched sequence patterns in plagl1 binding regions […]


DNA methylation based chromatin compartments and ChIP seq profiles reveal transcriptional drivers of prostate carcinogenesis

Genome Med
PMCID: 5463361
PMID: 28592290
DOI: 10.1186/s13073-017-0443-z

[…] 100-kb window, and these scores were compared for windows with different compartment calls as inferred from dna methylation data., processed data as h3k27ac chip-seq peaks positions (called with sole-search [], from []) mapped to the hg19 human genome were downloaded from gene expression omnibus (geo) [geo:gsm1249448]. the proportion of each 100-kb window that is covered by an lncap h3k27ac […]


Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells

Nucleic Acids Res
PMCID: 4872074
PMID: 26743005
DOI: 10.1093/nar/gkv1530

[…] were assessed after rinsing the plates with water., h3k27ac chip-seq data from hct116 cells (encode accession number encsr000eut) was downloaded from the ucsc genome browser and analyzed using the sole-search chip-seq peak calling program (,) using the following parameters (permutation:5; fragment:250; αvalue: 0.00010 = 1.0e-4; fdr: 0.00010 = 1.0e-4; peakmergedistance:0; […]


Functional annotation of colon cancer risk SNPs

Nat Commun
PMCID: 4200523
PMID: 25268989
DOI: 10.1038/ncomms6114

[…] cells included two replicates. to demonstrate the high quality of the data sets, we called peaks on each replicate of h3k27ac from hct116 and each replicate of h3k27ac from sigmoid colon using sole-search and compared the peak sets from the two replicates using the encode 40% overlap rule (after truncating both lists to the same number, 80% of the top 40% of one replicate must be found […]


Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes

Genome Biol
PMCID: 4203885
PMID: 25239471
DOI: 10.1186/s13059-014-0469-0

[…] via encode and were downloaded from the ucsc browser, accession number [ucsc: wgencodeeh000949]. all chip-seq data were mapped to hg19 using bwa (default parameters) and peaks were called using sole-search [,] with the following parameters: permutation:5; fragment:250; alphavalue: 0.00010 = 1.0e-4; fdr: 0.00010 = 1.0e-4; peakmergedistance:0; histoneblurlength:1200 for h3k4me3 and h3k27ac. […]


Differential regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros

Nat Immunol
PMCID: 3800053
PMID: 24013668
DOI: 10.1038/ni.2707

[…] throughput sequencing core. raw sequences were mapped by bowtie to the july 2007 annotation of mouse (mus musculus) genome data (mm9), and significant peaks over background were called using the sole-search software,. genome coverage visualization files were created with bedtools and uploaded to the uc santa cruz genome browser ( de novo motif analysis was performed […]

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Sole-Search institution(s)
Genome Center, University of California-Davis, Davis, CA, USA; Department of Computer Science, University of California-Davis, Davis, CA, USA; Department of Molecular and Cellular Biology, University of California-Davis, Davis, CA, USA; Department of Pharmacology, University of California-Davis, Davis, CA, USA
Sole-Search funding source(s)
National Institutes of Health (CA45250, 1U54HG004558, GM007377); the National Science Foundation (IIS- 0612326)

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