Internet Contig Explorer (iCE)—A Tool for
Visualizing Clone Fingerprint Maps
Christopher D. Fjell,1Ian Bosdet, Jacqueline E. Schein, Steven J.M. Jones,
and Marco A. Marra
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada
Fingerprinted clone physical maps have proven useful in various applications, supporting both whole-genome
and region-specific DNA sequencing as well as gene cloning studies. Fingerprint maps have been generated for
several genomes, including those of human, mouse, rat, the nematodes Caenorhabditis elegans and Caenorhabditis
briggsae, Arabidopsis thaliana and rice. Fingerprint maps of other genomes, including those of fungi, bacteria,
poplar, and the cow, are being generated. The increasing use of fingerprint maps in genomic research has
spawned a need in the research community for intuitive computer tools that facilitate viewing of the maps and
the underlying fingerprint data. In this report we describe a new Java-based application called iCE (Internet
Contig Explorer) that has been designed to provide views of fingerprint maps and associated data. Users can
search for and display individual clones, contigs, clone fingerprints, clone insert sizes and markers. Users can
also load into the software lists of particular clones of interest and view their fingerprints. iCE is being used at
our Genome Centre to offer up to the research community views of the mouse, rat, bovine, C. briggsae, and
several fungal genome bacterial artificial chromosome (BAC) fingerprint maps we have either completed or are
currently constructing. We are also using iCE as part of the Rat Genome Sequencing Project to manage our
provision of rat BAC clones for sequencing at the Human Genome Sequencing Center at the Baylor College of
DNA clone fingerprint maps (Olson et al. 1986; Sulston et al.
1988; Marra et al. 1997; Marra et al. 1999) have proven useful
in various genomics investigations and hence the demand for
these maps has increased steadily. Fingerprint maps either
have been or are being generated for the genomes of many
intensively studied organisms, including human (McPherson
et al. 2001), mouse (Gregory et al. 2002), the model plant A.
thaliana (Marra et al. 1999), the laboratory rat (J. Schein and
the BCCA Genome Sciences Centre, unpubl.), Caenorhabditis
elegans (Coulson et al. 1986, 1991), and Caenorhabditis briggsae
(Marra et al. 1997). In addition, fingerprint maps either have
been or are being generated for the genomes of organisms of
agricultural importance, including cow (J. Schein and the
BCCA Genome Sciences Centre, unpubl.), rice (Mao et al.
2000), sorghum (Klein et al. 2000), and corn (Coe et al. 2002).
Also under construction are fingerprint maps of the genomes
of fungal and bacterial pathogens, including those of C. neo-
formans (Schein et al. 2002) and Ustilago hordeii (J. Kronstad
and M. Marra, unpubl.), the fungus Magnaporthe grisea (Zhu et
al. 1999), and Chlamydia (I. Bosdet, M. Marra, and B. Brun-
ham, unpubl.). Fingerprint maps for additional genomes are
The software most heavily used for analysis of fingerprint
data and display of fingerprint maps is FPC (Soderlund 1997,
2000; http://www.genome.arizona.edu/software/fpc). This
powerful and versatile software package, running under UNIX
or LINUX, has become the standard for genome map con-
struction and editing. We offer via FTP our maps in FPC for-
mat, so researchers can download the data and view them
using a locally installed copy of the FPC program. However, as
a consequence of its power and versatility, FPC is complex
and this, coupled with the requirement of a UNIX-based ar-
chitecture to install and run the software, has presented dif-
ficulties for some investigators wishing to view clone finger-
print databases. In addition, the databases may be large (up to
several hundred megabytes in size) and may frequently
change as data are updated. In our experience many investi-
gators often wish only to search the fingerprint maps for spe-
cific clones or markers and view these and the genomic seg-
ments (contigs) to which they belong. Due to the increasing
use of the clone fingerprint approach to physical map con-
struction and the corresponding increases in both the number
of genomes mapped and the number of researchers requiring
access to these maps, we saw a need for a simplified Internet-
There are several existing services available to view physi-
cal maps via the Internet. Web-FPC offers a limited view of
physical maps similar to FPC for maps such as rice, maize,
sorghum, zebrafish, and Arabidopsis thaliana (http://
www.genome.arizona.edu/software/fpc/). Other sites such as
Ensembl (http://www.ensembl.org/) and NCBI (http://
www.ncbi.nlm.nih.gov/mapview/) also offer views of BAC
maps integrated with sequence and other information. How-
ever, these existing tools did not provide the full functionality
we desired and were not adaptable to the more distant future
needs we foresaw. Therefore, the Internet Contig Explorer
(iCE) was devised to fill this need.
The aim of iCE was not to recreate the broad scope of
functions available already in FPC. Instead, our goal was to
provide a viewing system sufficient to satisfy most of the in-
vestigators who wished to browse the fingerprint data and the
maps built from them without the requirement and overhead
of downloading and updating datasets. In designing iCE we
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/
1244 Genome Research
13:1244–1249 ©2003 by Cold Spring Harbor Laboratory Press ISSN 1088-9051/03 $5.00; www.genome.org
on Linux and Microsoft Windows 2000 on computers with an
Intel Pentium III processor and 512 MB RAM, and on Apple
computers running MacOS X. All contig, clone, and marker
data originate in FPC databases and are converted to the SQL
format using a custom application (fpc_sql) written in the C
We thank the many people who contributed to testing and
implementation of iCE at the Genome Sciences Centre.
Thanks to Justin Muir, Kirk Schoeffel, and Martin Krzywinski
for installing the iCE Web server. Thanks also to Steven Ness
for useful comments on an early version of the manuscript
and to Mike Holman at Washington University Genome Se-
quencing Center for helpful early discussions. This work was
funded by the National Human Genome Research Institute
(USA). We are grateful to the staff of the British Columbia
Cancer Agency Genome Sciences Centre for expert technical
and administrative assistance. M.A.M. is a Michael Smith
Foundation for Health Research Scholar.
The publication costs of this article were defrayed in part
by payment of page charges. This article must therefore be
hereby marked “advertisement” in accordance with 18 USC
section 1734 solely to indicate this fact.
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WEB SITE REFERENCES
http://www.genome.clemson.edu/fpc/; Web-based FPC physical
http://www.genome.arizona.edu/software/fpc/; FPC home page.
http://www.ensembl.org/; Ensembl genome browser.
http://www.ncbi.nlm.nih.gov/mapview/; NCBI Map Viewer.
http://ice.bcgsc.ca; iCE home page.
http://java.sun.com; JAVA home page, Sun Microsystems Inc.
http://www.borland.com; Borland Software Corp. (JBuilder vendor).
http://www.mysql.com; MySQL open source SQL database home
Received September 17, 2002; accepted in revised form March 14, 2003.
Internet Contig Explorer