4 Visualising oligonucleotide and consensus sequence densities 4 4.1 Preparing input sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 4.2 Plotting dinucleotide density maps . . . . . . . . . . . . . . . . . . . . . . 6 4.3 Plotting average oligonucleotide profiles . . . . . . . . . . . . . . . . . . . . 10 4.4 Plotting consensus sequence density map . . . . . . . . . . . . . . ...

BACKGROUND Diabetic nephropathy (DN) is a complex and chronic metabolic disease that evolves into a progressive fibrosing renal disorder. Effective transcriptomic profiling of slowly evolving disease processes such as DN can be problematic. The changes that occur are often subtle and can escape detection by conventional oligonucleotide DNA array analyses. METHODOLOGY/PRINCIPAL FINDINGS We exa...

Variation in tissue sample preparation leads to variation across the Transcriptome not just between experiments but to between individual microarrays. Normalisation is essential before data from different arrays can be compared. Quantile normalisation can be used to force data from a single GeneChip to take a given distribution. However quantile normalisation can be blind to the consistent spat...

BACKGROUND Onychomycosis is a fungal infection of nails, leading to the gradual destruction of the nail plate. Treatment of onychomycosis may need long-time oral antifungal therapy that can have potential side effects, thus accurate diagnosis of the disease before treatment is important. Culture for diagnosis of onychomycosis is time-consuming and has high false-negative rates. To expedite the ...

By employing in gel competitive reassociation, which distinguishes two DNA preparations, to clone anonymous DNA fragments with altered primary structure, we isolated a clone (BL-1) from a rat DNA which gave an extra, apparently altered, DNA band in a specific tissue (brain) when we used it as a probe for Southern hybridization. The sequence of BL-1 was very similar to a portion of LINE, a highl...

Transgenic mouse alleles continue to be used heavily in biomedical research (1). Transgenes insert into the genome at random sites, typically in a tandem array of 1 to 20 copies. Both Southern blot analysis and real-time PCR can be used for determining the zygosity of transgenes, but each have practical and technical limitations (2–4). Here we describe a robust, easily implemented method for de...

Oligonucleotide arrays capable of detecting single nucleotide polymorphisms (SNPs) from amplified nucleic acid have many applications. The expected SNP is usually placed approximately in the center of the probe to ensure the maximum shift in Tm between complementary and SNP sequences. Unfortunately, different short probes (< 30 bases) selected using widely accepted criteria do not perform consi...

A human cytomegalovirus mutant that was isolated for resistance (10-fold) to the antisense oligonucleotide fomivirsen (ISIS 2922) exhibited cross-resistance to a modified derivative of fomivirsen with an identical base sequence but little or no resistance to an oligonucleotide with an unrelated sequence. No changes in the mutant's DNA corresponding to the fomivirsen target sequence were found.

Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1000 to several million base pairs. Among current array-based CNV detection platforms, long-oligonucleotide arrays promise the highest resolution. However, the performance of currently available analytical tools suffers when applied to these data because of the low...