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Bioinformatics Advance Access originally published online on June 1, 2006
Bioinformatics 2006 22(19):2437-2438; doi:10.1093/bioinformatics/btl273
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

PROBER: oligonucleotide FISH probe design software

Nicholas Navin 1,2,*, Vladimir Grubor 2, Jim Hicks 2, Evan Leibu 2, Elizabeth Thomas 1, Jennifer Troge 2, Michael Riggs 2, Pär Lundin 3, Susanne Månér 3, Jonathan Sebat 2, Anders Zetterberg 3 and Michael Wigler 2

1 Watson School of Biological Sciences, Cold Spring Harbor NY 11724, USA
2 Cold Spring Harbor Laboratory, Cold Spring Harbor NY 11724, USA
3 Karolinska Institutet, Cancer Center Karolinska Stockholm, Sweden

*To whom correspondence should be addressed.

PROBER is an oligonucleotide primer design software application that designs multiple primer pairs for generating PCR probes useful for fluorescence in situ hybridization (FISH). PROBER generates Tiling Oligonucleotide Probes (TOPs) by masking repetitive genomic sequences and delineating essentially unique regions that can be amplified to yield small (100–2000 bp) DNA probes that in aggregate will generate a single, strong fluorescent signal for regions as small as a single gene. TOPs are an alternative to bacterial artificial chromosomes (BACs) that are commonly used for FISH but may be unstable, unavailable, chimeric, or non-specific to small (10–100 kb) genomic regions. PROBER can be applied to any genomic locus, with the limitation that the locus must contain at least 10 kb of essentially unique blocks. To test the software, we designed a number of probes for genomic amplifications and hemizygous deletions that were initially detected by Representational Oligonucleotide Microarray Analysis of breast cancer tumors.

Availability: http://prober.cshl.edu

Contact: navin{at}cshl.edu

Received on February 22, 2006; revised on May 6, 2006; accepted on May 24, 2006

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