PROBER: oligonucleotide FISH probe design software

Navin, N. E., Grubor, V., Hicks, J. B., Leibu, E., Thomas, E., Troge, J., Riggs, M., Lundin, P., Månér, S., Sebat, J., Zetterberg, A., Wigler, M. H. (October 2006) PROBER: oligonucleotide FISH probe design software. Bioinformatics, 22 (19). pp. 2437-8. ISSN 1460-2059 (Electronic)

[img]
Preview
PDF (Paper)
PROBER oligonucleotide FISH probe design software.pdf - Published Version

Download (107Kb) | Preview
URL: http://www.ncbi.nlm.nih.gov/pubmed/16740623
DOI: 10.1093/bioinformatics/btl273

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. AVAILABILITY: http://prober.cshl.edu

Item Type: Paper
Uncontrolled Keywords: Algorithms Base Sequence Chromosome Mapping methods Computer Aided Design DNA Probes genetics Equipment Design In Situ Hybridization Fluorescence instrumentation methods Molecular Sequence Data Sequence Alignment methods Sequence Analysis DNA methods Software
Subjects: Investigative techniques and equipment > cloning > PCR
Investigative techniques and equipment > assays > cloning > PCR

bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > oligonucleotide primer
CSHL Authors:
Communities: CSHL labs > Hicks lab
CSHL labs > Sebat lab
CSHL labs > Wigler lab
Watson School > Publications
Depositing User: CSHL Librarian
Date: 1 October 2006
Date Deposited: 05 Apr 2012 15:42
Last Modified: 26 Sep 2014 14:07
Related URLs:
URI: http://repository.cshl.edu/id/eprint/26035

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving