Abstract: The invention provides a method for detecting and quantifying the amount of target molecules, such as nucleic acids or proteins in a sample. The target molecules are first recognized and bounded by target-specific probes, generally nucleic acids or proteins that bind specifically to the targets, each of which is labeled with a short single-stranded nucleic acid probe, either DNA or RNA, with distinct molecular weight. This label is called an oligonucleotide mass tag. One or several standard oligonucleotide sequences can be designed with similar sequence but distinct molecular weight to those oligonucleotide mass tags. Then the oligonucleotide mass tags associated with bounded probes and the standard sequences are co-amplified using a pair of common primers. The presence and/or amount of each oligonucleotide mass tag, which corresponds to the amount of corresponding target molecule, is determined by a primer extension reaction and quantification of the primer extension product.

Abstract: The invention provides a method for detecting and quantifying the amount of target molecules, such as nucleic acids or proteins in a sample. The target molecules are first recognized and bounded by target-specific probes, generally nucleic acids or proteins that bind specifically to the targets, each of which is labeled with a short single-stranded nucleic acid probe, either DNA or RNA, with distinct molecular weight. This label is called an oligonucleotide mass tag. One or several standard oligonucleotide sequences can be designed with similar sequence but distinct molecular weight to those oligonucleotide mass tags. Then the oligonucleotide mass tags associated with bounded probes and the standard sequences are co-amplified using a pair of common primers. The presence and/or amount of each oligonucleotide mass tag, which corresponds to the amount of corresponding target molecule, is determined by a primer extension reaction and quantification of the primer extension product.

Abstract: A method and apparatus transforms typically differing length text string representations (i.e., sequences) of biological fragments into uniform length representations. A comparison database stores a predefined number of known biological sequences. A comparison routine compares and scores a subject sequence against each known sequence in the database. Each individual score (one for each known sequence in the database) serves as a vector element forming a fixed length vector representation of the subject sequence. Vector length equals the predefined number of known biological sequences in the database. Scoring is a probability or an occurrence count of the known biological sequence in the subject sequence.

Abstract: Computer based apparatus and method automates gene prediction in a subject genomic sequence. A plurality of expert systems provide preliminary or intermediate gene predictions. A Bayesian network combiner combines the intermediate gene predictions and forms a final gene prediction. The final gene prediction accounts for dependencies between individual expert systems and dependencies between adjacent parts of the subject genomic sequence.

Abstract: Computer based apparatus and method automates gene prediction in a subject genomic sequence. A plurality of expert systems provide preliminary or intermediate gene predictions. A Bayesian network combiner combines the intermediate gene predictions and forms a final gene prediction. The final gene prediction accounts for dependencies between individual expert systems and dependencies between adjacent parts of the subject genomic sequence.

Abstract: Computer based apparatus and method automates gene prediction in a subject genomic sequence. A plurality of expert systems provide preliminary or intermediate gene predictions. A Bayesian network combiner combines the intermediate gene predictions and forms a final gene prediction. The final gene prediction accounts for dependencies between individual expert systems and dependencies between adjacent parts of the subject genomic sequence.