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iCE specifications

Information


Unique identifier OMICS_23259
Name iCE
Alternative name Internet Contig Explorer
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Database management system MySQL
Computer skills Medium
Version 3.5.0
Stability Stable
Requirements
JRE
Maintained Yes

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Versioning


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Maintainer


  • person_outline Christopher Fjell

Publication for Internet Contig Explorer

iCE citations

 (4)
library_books

Major Histocompatibility Complex Genes Map to Two Chromosomes in an Evolutionarily Ancient Reptile, the Tuatara Sphenodon punctatus

2015
PMCID: 4502378
PMID: 25953959
DOI: 10.1534/g3.115.017467

[…] with EcoRI/EcoRV () was performed by the Genome Sciences Center, British Columbia Cancer Agency, Canada. Contigs were assembled with FPC with a tolerance of 7 and cutoff of 1e-12 and visualized using Internet Contig Explorer v3.5 (). […]

library_books

Regulation and expression of sexual differentiation factors in embryonic and extragonadal tissues of Atlantic salmon

2011
BMC Genomics
PMCID: 3034696
PMID: 21232142
DOI: 10.1186/1471-2164-12-31

[…] II restriction digests of the isolated clones to in silico digests for each BAC. BAC clones were chosen based on the physical BAC fingerprint map for Atlantic salmon that is publicly available on the internet Contig Explorer (iCE) version 3.5 []. The BAC end sequence information, that is available in ASalBase [], was also used for selection of the BAC clones. […]

library_books

Evolution of duplicated IgH loci in Atlantic salmon, Salmo salar

2010
BMC Genomics
PMCID: 2996982
PMID: 20813058
DOI: 10.1186/1471-2164-11-486

[…] g of 1 × SSC and 0.1% SDS. Filters were visualized using BioMax film (Kodak). BAC clones were chosen based on the physical BAC fingerprint map for Atlantic salmon [] that is publicly available on the internet Contig Explorer (iCE) version 3.5 []. The BAC end sequence information, that is available in ASalBase [], was also used for selection of the BAC clones. BAC shotgun libraries were constructed […]

library_books

Isolation, characterization and comparison of Atlantic and Chinook salmon growth hormone 1 and 2

2008
BMC Genomics
PMCID: 2584663
PMID: 18980692
DOI: 10.1186/1471-2164-9-522

[…] HindIII restriction digests of the isolated clones to in silico digests for each BAC. The entire Salmo salar genome BAC library has been digested by HindIII and fragment profiles are available on the internet Contig Explorer version 3.4 (iCE 3.4) database []. Fingerprinting of the CS BACs was carried out by SnaPshot (ABI) labeling of restriction-digested fragments and samples were analyzed on an A […]

Citations

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iCE institution(s)
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada

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