title: PROBER: oligonucleotide FISH probe design software.
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 (100-2000 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
authors.affiliation: Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA. navin@cshl.edu
authors.forename: Nicholas
authors.initials: N
authors.lastname: Navin
authors.forename: Vladimir
authors.initials: V
authors.lastname: Grubor
authors.forename: Jim
authors.initials: J
authors.lastname: Hicks
authors.forename: Evan
authors.initials: E
authors.lastname: Leibu
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Thomas
authors.forename: Jennifer
authors.initials: J
authors.lastname: Troge
authors.forename: Michael
authors.initials: M
authors.lastname: Riggs
authors.forename: Pär
authors.initials: P
authors.lastname: Lundin
authors.forename: Susanne
authors.initials: S
authors.lastname: Månér
authors.forename: Jonathan
authors.initials: J
authors.lastname: Sebat
authors.forename: Anders
authors.initials: A
authors.lastname: Zetterberg
authors.forename: Michael
authors.initials: M
authors.lastname: Wigler
mesh_terms: 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
chemical_list: D015342:DNA Probes