Abstract: Devices formed as optically readable substrates are provided having a high feature density (e.g., attachment or deposition sites) in arrays comprising macromolecules, specifically amplicons, and devices and methods are provided for analysis of target nucleic acids having an undetermined sequence.

Abstract: The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include template nucleic acids with stabilizing sequences. The present invention also includes concatemers formed from template nucleic acids that have stabilizing sequences, arrays of such concatemers, as well as methods for identifying and detecting sequences of such concatemers.

Abstract: Methods for linearly amplifying mRNA to produce antisense RNA are provided. In the subject methods, mRNA is converted to double-stranded cDNA using a promoter-primer having a poly-dT primer site linked to a promoter sequence so that the resulting double-stranded cDNA is recognized by an RNA polymerase. The resultant double-stranded cDNA is then transcribed into antisense RNA in the presence of a reverse transcriptase that is rendered incapable of RNA-dependent DNA polymerase activity during this transcription step. The subject methods find use a variety of different applications in which the preparation of linearly amplified amounts of antisense RNA is desired. Also provided are kits for practicing the subject methods.

Abstract: Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or microarray, comprising selecting a plurality of candidate probes, forming a plurality of clusters from the plurality of candidate probes according to hybridization characteristics of the candidate probes, forming at least one SuperCluster from the clusters; and selecting at least one probe from each SuperCluster for the probe array.

Abstract: Methods of identifying a sequence of a probe, e.g., a biopolymeric probe, such as a nucleic acid, that is suitable for use as a surface immobilized normalization probe on a nucleic acid array are provided. A feature of the subject methods is that a set of computationally determined initial candidate sequences are empirically evaluated to obtain functional data that is then employed to evaluate the candidate sequences for suitability as normalization probes. Sequences identified as suitable for use as normalization probes according to the subject methods are ones that do not cluster with other probes of the candidate set, exhibit high signal intensity and exhibit substantially no differential expression across a large number of samples. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same.

Abstract: Methods are disclosed for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides is identified. The unique oligonucleotides are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. At least one parameter that is independently predictive of the ability of each of the oligonucleotides of the set to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotides. A subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified based on the evaluation of the parameter. Oligonucleotides in the subset are identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The method may be carried out with the aid of a computer.