Abstract: DNA sequences are analyzed using latent semantic analysis. A set of nucleotide sequences is received in which the set has a first number of sequences. A set of basis vectors is determined, in which the set has a second number of basis vectors, the second number being smaller than the first number. Each basis vector represents a specific combination of predetermined nucleotide segments. For each of the nucleotide sequences, an approximate representation of the nucleotide sequence is determined based on a combination of the basis vectors. For each pair of nucleotide sequences, a distance between the pair of nucleotide sequences is determined according the distance between the approximate representation of the pair of nucleotide sequences. The set of nucleotide sequences are classified based on the distances between the pairs of nucleotide sequences.

Abstract: The present invention permits identification of biological materials following recovery of DNA using standard techniques by comparing a mathematical characterization of the unknown sequence with the mathematical characterization of DNA sequences of known genera and species. The clinical identification of infectious organisms is required for accurate diagnosis and selection of antimicrobial therapeutics. The invention allows an ab initio approach with the potential for rapid identification of biological materials of unknown origin. The approach provides for identification and classification of emergent or new organisms without previous phenotypic identification. The technique may also be used in monitoring situations where the need exists for classification of material into broad categories of bacteria which could have an immediate impact on bio-terrorism prevention.

Abstract: DNA sequences are analyzed using latent semantic analysis. A set of nucleotide sequences is received in which the set has a first number of sequences. A set of basis vectors is determined, in which the set has a second number of basis vectors, the second number being smaller than the first number. Each basis vector represents a specific combination of predetermined nucleotide segments. For each of the nucleotide sequences, an approximate representation of the nucleotide sequence is determined based on a combination of the basis vectors. For each pair of nucleotide sequences, a distance between the pair of nucleotide sequences is determined according the distance between the approximate representation of the pair of nucleotide sequences. The set of nucleotide sequences are classified based on the distances between the pairs of nucleotide sequences.

Abstract: The present invention permits identification of biological materials following recovery of DNA using standard techniques by comparing a mathematical characterization of the unknown sequence with the mathematical characterization of DNA sequences of known genera and species. The clinical identification of infectious organisms is required for accurate diagnosis and selection of antimicrobial therapeutics. The invention allows an ab initio approach with the potential for rapid identification of biological materials of unknown origin. The approach provides for identification and classification of emergent or new organisms without previous phenotypic identification. The technique may also be used in monitoring situations where the need exists for classification of material into broad categories of bacteria which could have an immediate impact on bio-terrorism prevention.

Abstract: Methods and kits for the identification of a primase trinucleotide initiation site and for the identification of compounds which modulate bacterial primase activity are provided.

Abstract: Disclosed is a system and method for joint source-channel encoding, symbol decoding and error correction, preferably utilizing an arithmetic encoder with operational error detection space; and a combination sequential, and arithmetic, encoded symbol decoder structure.

Abstract: The present invention provides a new algorithm for assembling fragments from a long DNA sequence. The algorithm of the invention solves simultaneously fragment assembly-related problems such as the fragment orientation, overlap and layout phases. This is achieved by clustering fragments with respect to their Average Mutual Information (AMI) profiles using the k-means algorithm.

Abstract: Disclosed is a system and method for joint source-channel encoding, symbol decoding and error correction, preferably utilizing an arithmetic encoder with operational error detection space; and a combination sequential, and arithmetic, encoded symbol decoder means.

Abstract: Disclosed is a A system and method for joint source-channel encoding, symbol decoding and error correction, preferably utilizing an arithmetic encoder with operational error detection space; and a combination sequential, and arithmetic, encoded symbol decoder structure.