Abstract: Genetic sequence data occurring in genome sequences is represented for efficient access of the sequence information in a defined storage scheme. A described replet-sequence matrix data structure allows the compression and efficient access of sequence information. The data structure allows the dynamic change of ontology: the replet-information table can evolve by adding, updating, removing replets, and the set of replets present in the table represent the ontology at the moment. The data structure enables the sequence information to be processed in parallel, and also enables multiple views of the sequence data to exist along with replet specific information.

Abstract: Genetic sequence data occurring in genome sequences is represented for efficient access of the sequence information in a defined storage scheme. A described replet-sequence matrix data structure allows the compression and efficient access of sequence information. The data structure allows the dynamic change of ontology: the replet-information table can evolve by adding, updating, removing replets, and the set of replets present in the table represent the ontology at the moment. The data structure enables the sequence information to be processed in parallel, and also enables multiple views of the sequence data to exist along with replet specific information.

Abstract: A method and system for finding in a DNA sequence, a gene represented by an ordered set of marker strings is disclosed. Sub-strings in the DNA sequence matching each marker string are identified. In a set ordered via occurrence of the marker strings in the ordered set of marker strings, the score and position of each sub-string whose score satisfies a matching constraint is recorded. For each except the last marker string, directed links are created between each identified sub-string that matches the marker string and any identified sub-strings that match the subsequent marker string, subject to the directed links satisfying an inter-marker length constraint. Traced are all paths that connect each identified sub-string that matches the first marker string to an identified sub-string that matches the last marker string using the directed links. The paths satisfy a sequence length constraint and are stored in memory of a computer system.

Abstract: A method, system and computer program product for identifying occurrences of a sequence of ordered marker strings in a string are disclosed. The method includes the steps of identifying sub-strings in the string that match the marker, for each marker string except the last marker string in the ordered sequence of marker strings creating directed links between a sub-string that matches a particular marker string and all the sub-strings that match a subsequent marker string in the ordered sequence of marker strings, and identifying occurrences of the sequence in the string by tracing one or more corresponding paths from each sub-string that matches the first marker string to all sub-strings that match the last marker string by following the directed links. The method, system and computer program product disclosed particularly relate to finding a gene in a DNA sequence.

Abstract: A method, system and computer program product for identifying occurrences of a sequence of ordered marker strings in a string are disclosed. The method includes the steps of identifying sub-strings in the string that match the marker, for each marker string except the last marker string in the ordered sequence of marker strings creating directed links between a sub-string that matches a particular marker string and all the sub-strings that match a subsequent marker string in the ordered sequence of marker strings, and identifying occurrences of the sequence in the string by tracing one or more corresponding paths from each sub-string that matches the first marker string to all sub-strings that match the last marker string by following the directed links. The method, system and computer program product disclosed particularly relate to finding a gene in a DNA sequence.