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Bioinformatics Advance Access published online on June 1, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl273
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© 2006 The Author(s)
Received February 22, 2006
Revised May 6, 2006
Accepted May 24, 2006

Applications note

PROBER : oligonucleotide FISH probe design software

Nicholas Navin 1 *, Vladimir Grubor 2, Jim Hicks 2, Evan Leibu 2, Elizabeth Thomas 3, Jennifer Troge 2, Michael Riggs 2, Pär Lundin 4, Susanne Månér 4, Jonathan Sebat 2, Anders Zetterberg 4, and Michael Wigler 2

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

* To whom correspondence should be addressed.
Nicholas Navin, E-mail: navin{at}cshl.edu


  Abstract

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 (100-2000bp) 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 (10-100kb) genomic regions. PROBER can be applied to any genomic locus, with the limitation that the locus must contain at least 10kb 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 (ROMA) of breast cancer tumors.

Availability: http://prober.cshl.edu.

Associate Editor: Martin Bishop
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