PROBER: oligonucleotide FISH probe design software.
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.


BACKGROUND
http://prober.cshl.edu
Navin
Nicholas
N
Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA. navin@cshl.edu
Grubor
Vladimir
V
Hicks
Jim
J
Leibu
Evan
E
Thomas
Elizabeth
E
Troge
Jennifer
J
Riggs
Michael
M
Lundin
Pär
P
Månér
Susanne
S
Sebat
Jonathan
J
Zetterberg
Anders
A
Wigler
Michael
M
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D017076:Computer-Aided Design; D015342:DNA Probes / Q000235:genetics*; D004867:Equipment Design; D017404:In Situ Hybridization, Fluorescence / Q000295:instrumentation / Q000379:methods*; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D015342:DNA Probes