Abstract: The present invention discloses a designing strategy for constructing a set of probes useful for analyzing all or most prokaryotic and eukaryotic genomes. A set of capture probes with optimal fingerprinting properties and highly representative of all possible sequences of an organism can be selected by six sequential steps. Fingerprinting potential of such probes is validated by phylogenetic analysis, which generates results that strongly correlate with phylogenetic trees produced by sequence alignment. The probes generated by the instant methods can be used for detecting an organism, for establishing phylogenetic relationships between different organisms, for detection of single nucleotide polymorphisms and a wide variety of other applications that require genetic analysis.

Abstract: Software for designing optimized sets of oligonucleotide probes for use in genosensors (oligonucleotide microarrays) is disclosed. The selection of probe sequences is based on multiple criteria including thermal stability of the probe-target pairs, similarity degree of the probes with respect to other DNA sequences, and evaluation of the secondary structure of target molecules. The programs were written in the programming language Borland Delphi by means of Object-Oriented Programming (OOP) techniques. The Genosensor Probe Design computer program disclosed herein facilitates the design of optimized arrays of probes which accurately represents the characteristics of the nucleic acid molecule under study, such as its identity or its differences in sequence or abundance with respect to other molecules.

Abstract: Software for designing optimized sets of oligonucleotide probes for use in genosensors (oligonucleotide microarrays) is disclosed. The selection of probe sequences is based on multiple criteria including thermal stability of the probe-target pairs, similarity degree of the probes with respect to other DNA sequences, and evaluation of the secondary structure of target molecules. The programs were written in the programming language Borland Delphi by means of Object-Oriented Programming (OOP) techniques. The Genosensor Probe Design computer program disclosed herein facilitates the design of optimized arrays of probes which accurately represents the characteristics of the nucleic acid molecule under study, such as its identity or its differences in sequence or abundance with respect to other molecules.

Abstract: The disclosed invention provides a novel method for analyzing genomic DNA and expressed sequences using auxiliary oligonucleotides, preannealed to the single-stranded target nucleic acid to form a partially duplex target molecule, offers several advantages in the analysis of nucleic acid sequences by hybridization to genosensor arrays or “DNA chips”. Also provided is a method for directly analyzing and comparing patterns of gene expression at the level of transcription in different cellular samples.