PROBER: oligonucleotide FISH probe design software
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PROBER: oligonucleotide FISH probe design software
UNLABELLED 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 ...
متن کاملEmpirical establishment of oligonucleotide probe design criteria.
Criteria for the design of gene-specific and group-specific oligonucleotide probes were established experimentally via an oligonucleotide array that contained perfect match (PM) and mismatch probes (50-mers and 70-mers) based upon four genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were tested. Little hybridizatio...
متن کاملComprehensive viral oligonucleotide probe design using conserved protein regions
Oligonucleotide microarrays have been applied to microbial surveillance and discovery where highly multiplexed assays are required to address a wide range of genetic targets. Although printing density continues to increase, the design of comprehensive microbial probe sets remains a daunting challenge, particularly in virology where rapid sequence evolution and database expansion confound static...
متن کاملEvaluating oligonucleotide properties for DNA microarray probe design
Most current microarray oligonucleotide probe design strategies are based on probe design factors (PDFs), which include probe hybridization free energy (PHFE), probe minimum folding energy (PMFE), dimer score, hairpin score, homology score and complexity score. The impact of these PDFs on probe performance was evaluated using four sets of microarray comparative genome hybridization (aCGH) data,...
متن کاملThe oligonucleotide probe database.
The use of oligonucleotide hybridization probes and PCR primers has become widespread in microbial ecology and environmental microbiology (for reviews, see references 3, 5, 7, 17, and 21), and descriptions of probe applications are abundant in the literature. We have encountered, however, a number of difficulties when relying on the literature for information on probes and primers: (i) probe de...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2006
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btl273