PMID- 16740623
OWN - NLM
STAT- MEDLINE
DCOM- 20061106
LR  - 20191210
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Linking)
VI  - 22
IP  - 19
DP  - 2006 Oct 1
TI  - PROBER: oligonucleotide FISH probe design software.
PG  - 2437-8
AB  - 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
FAU - Navin, Nicholas
AU  - Navin N
AD  - Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA. 
      navin@cshl.edu
FAU - Grubor, Vladimir
AU  - Grubor V
FAU - Hicks, Jim
AU  - Hicks J
FAU - Leibu, Evan
AU  - Leibu E
FAU - Thomas, Elizabeth
AU  - Thomas E
FAU - Troge, Jennifer
AU  - Troge J
FAU - Riggs, Michael
AU  - Riggs M
FAU - Lundin, Par
AU  - Lundin P
FAU - Maner, Susanne
AU  - Maner S
FAU - Sebat, Jonathan
AU  - Sebat J
FAU - Zetterberg, Anders
AU  - Zetterberg A
FAU - Wigler, Michael
AU  - Wigler M
LA  - eng
GR  - 5R01-CA078544-07/CA/NCI NIH HHS/United States
PT  - Evaluation Study
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20060601
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
RN  - 0 (DNA Probes)
SB  - IM
MH  - *Algorithms
MH  - Base Sequence
MH  - Chromosome Mapping/*methods
MH  - Computer-Aided Design
MH  - DNA Probes/*genetics
MH  - Equipment Design
MH  - In Situ Hybridization, Fluorescence/instrumentation/*methods
MH  - Molecular Sequence Data
MH  - Sequence Alignment/methods
MH  - Sequence Analysis, DNA/*methods
MH  - *Software
EDAT- 2006/06/03 09:00
MHDA- 2006/11/07 09:00
CRDT- 2006/06/03 09:00
PHST- 2006/06/03 09:00 [pubmed]
PHST- 2006/11/07 09:00 [medline]
PHST- 2006/06/03 09:00 [entrez]
AID - btl273 [pii]
AID - 10.1093/bioinformatics/btl273 [doi]
PST - ppublish
SO  - Bioinformatics. 2006 Oct 1;22(19):2437-8. doi: 10.1093/bioinformatics/btl273. 
      Epub 2006 Jun 1.