CAPweb protocols

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CAPweb specifications

Information


Unique identifier OMICS_02575
Name CAPweb
Alternative name CGH-Array Analysis Platform
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline CAPweb Team <>
  • person_outline CAP web Team <>

Additional information


Tutorial: http://bioinfo-out.curie.fr/tutorial/CAPweb/capweb_tutorial.html

Publication for CGH-Array Analysis Platform

CAPweb in pipeline

2010
PMCID: 3966227
PMID: 24710094
DOI: 10.3390/genes1030388

[…] sunnyvale, ca, usa). further data analysis and visualization of cgh profiles were carried out as described by unger et al. [] and bauer et al. [] using the web-based array cgh evaluation platform capweb [,] and the array data visualization tool vamp []., chromosome preparations were needed for sky and dicentric analysis as well as for testing bac clone specificity for fish. for metaphase […]


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CAPweb in publications

 (6)
PMCID: 3829972
PMID: 24260468
DOI: 10.1371/journal.pone.0080741

[…] were spotted in triplicate on ultragaps slides (corning). the probes were prepared and hybridized as previously described [27]. the data were analyzed with software developed at institut curie (capweb, http://bioinfo-out.curie.fr/capweb/). cyanine-5/cyanine-3 ratios between 0.8 and 1.2 were considered as normal status and ratios >1.2 and <0.8 were considered as gains and losses, […]

PMCID: 3528765
PMID: 23284877
DOI: 10.1371/journal.pone.0052079

[…] for chromosome bands using the msigdb positional gene sets , . centroid-linkage hierarchical clustering was performed in cluster 3.0 and visualized in treeview . array cgh data was normalized with capweb software and genomic alterations were visualized with vamp software using the same thresholds as previously described . snp data were normalized with illumina genome studio software v2010.1 […]

PMCID: 3558323
PMID: 23186559
DOI: 10.1186/1755-8794-5-54

[…] a median of 0.5 mb between clones. bac clones are spotted in quadruplicate. hybridizations were performed according to the manufacturer’s recommendations (see additional file )., data analysis, the capweb (copy number array analysis platform on the web) developed by institut curie (capweb, http://bioinfo-out.curie.fr/capweb/) was used for normalization (manor package), segmentation […]

PMCID: 3097344
PMID: 20820870
DOI: 10.1007/s11060-010-0380-9

[…] genome of each megabase. arrays were washed and scanned using a 4000b scanner (axon, union city, ca, usa). images were analyzed with the genepix6.0 software (axona). data were processed through the capweb platform to obtain cy5/cy3 fluorescence ratios and status (gained, lost, amplified or normal) for each bac []., fish experiments were conducted as previously reported []. briefly, probes […]

PMCID: 2949656
PMID: 20712882
DOI: 10.1186/bcr2626

[…] usa) and acquired images were analyzed with genepix pro 5.1 image analysis software to perform segmentation and to determine the mean intensities for the cy3 and cy5 signals of each bac clone., the capweb (copy number array analysis platform on the web) platform developed by institut curie [] was used for normalization (manor package), gain, loss or normal clone status assignment and breakpoint […]


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CAPweb institution(s)
Institut Curie, Service Bioinformatique, Paris, France
CAPweb funding source(s)
Supported by the Institut Curie, the Centre National de la Recherche Scientifique, the Canceropole Ile-de-France, the Region Ile-de-France and the association ‘Courir pour la vie, Courir pour Curie’.

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