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Genome Surveyor specifications

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Unique identifier OMICS_12881
Name Genome Surveyor
Interface Web user interface
Restrictions to use None
Input data CRM sequences
Input format FASTA
Computer skills Basic
Version 2.0
Stability No
Maintained No

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Publication for Genome Surveyor

Genome Surveyor citations

 (4)
library_books

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

2015
Nucleic Acids Res
PMCID: 4417154
PMID: 25791631
DOI: 10.1093/nar/gkv195

[…] we created motif score profiles from a collection of motifs for 325 distinct fruitfly tfs that were characterized with the bacterial 1-hybrid (b1h) technology () and made these available through the genome surveyor interface [http://veda.cs.uiuc.edu/gs]. our motif score profiles were calculated with the stubb tool (), which integrates any number of strong or weak predicted sites to estimate […]

library_books

Use of a Drosophila Genome Wide Conserved Sequence Database to Identify Functionally Related cis Regulatory Enhancers

2011
Dev Dyn
PMCID: 3243966
PMID: 22174086
DOI: 10.1002/dvdy.22728

[…] the kr_cd1 gap enhancer as the input csc (). it is important to point out that cis-decoder search protocols make direct use of csc information for enhancer prediction, while other resources, such as genome surveyor (kazemian et al., ), use site conservation as a criterion, but do not provide information to infer enhancer boundaries. given that multiple enhancer prediction programs that employ […]

library_books

Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

2010
PLoS Biol
PMCID: 2923081
PMID: 20808951
DOI: 10.1371/journal.pbio.1000456

[…] this computation is performed using a new “upward-downward” algorithm that scales linearly with the number of species. these single and multi-species motif profiles are made available through the “genome surveyor” interface at http://veda.cs.uiuc.edu/lmcrm/., we used published chip-on-chip data for eight tfs (bcd, cad, gt, hb, kni, kr, hkb, and tll) , to compare the ability of different motif […]

library_books

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one hybrid system

2008
Nucleic Acids Res
PMCID: 2377422
PMID: 18332042
DOI: 10.1093/nar/gkn048

[…] genomes generates similar plots indicating that our pwms should have utility for the prediction of crms within related species (supplementary figure 8)., we developed a new genome analysis tool, genome surveyor, to rapidly search for putative crms based on the presence of overrepresented binding sites for a combination of tfs. a simple scoring function was chosen based on its ability […]


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Genome Surveyor institution(s)
Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
Genome Surveyor funding source(s)
This work was supported in part by grants by the National Institute of Health (grant R01HG004744-01, grant R01GM085233-01).

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