System and method for searching and processing databases comprising named annotated text strings

A method for searching a genetic sequence database comprising a plurality of loci, each locus having a unique name, one or more annotations, and genetic sequence data represented as an ordered text string, the genetic database being stored in one or more database files, the method comprising the steps of:

• assigning a unique ID for each locus;
• assigning an annotation identifier for each predefined annotation type;
• constructing a parsed skeleton file associated with each of the database files, wherein each entry in the parsed skeleton file is associated with a particular locus and comprises a length and offset for each of the annotations and the genetic sequence data within the particular locus;
• building an index file associated with each of the database files, wherein each entry in the index file comprises an offset and length into a database file for each locus and an offset and length of the corresponding entry in the parsed skeleton file;
• selecting a portion of the genetic database in which to conduct a search;
• constructing an input hits list comprising the unique ID of each locus identified in said portion;
• specifying a search key comprising one or more keywords and one or more annotation types;
• performing a first database search using the input hits list and the search key;
• and
• outputting matches into a results hits list.

A system for searching a genetic sequence database comprising loci, each locus having a unique name, one or more annotations, and an ordered text string, the genetic sequence database being stored in one or more database files, the system comprising:

• a global index file generator coupled to the genetic sequence database for assigning a unique ID for each locus;
• an annotation definition module coupled to the genetic sequence database for assigning an annotation identifier for each predefined annotation type;
• a parsed skeleton file generator coupled to the genetic sequence database for constructing a parsed skeleton file associated with each of the database files, wherein each entry in the parsed skeleton file is associated with a particular locus and comprises one or more searchable object names, a length and an offset for each searchable object within the particular locus;
• and
• an index file generator coupled to the genetic sequence database for building an index file associated with each of the database files, wherein each entry in the index file comprises an offset and length into a database file for each locus and an offset and length of the corresponding entry in the parsed skeleton file.

A method for performing a context search on a genetic sequence database comprising loci, each locus having a unique name, one or more annotations, and an ordered text string, the genetic sequence database being stored in one or more database files, the method comprising the steps of:

• reading an ordered string;
• partitioning the ordered string into a plurality of sub-strings each marked either target or context;
• specifying one or more context relationships;
• searching for sub-strings marked target within regions that satisfy the specified context relationships;
• storing matches found in said searching step;
• and
• marking each sub-string found in said searching step with its associated context;
• wherein said storing and marking steps comprise the steps of:
• creating a results hits list comprising an array wherein each entry of the array comprises an iref number, a type field, and mark field;
• storing a pointer within each mark field that points to the associated context reference entry.

A computer program product comprising a computer useable medium having computer program logic stored therein, said computer program logic for enabling a computer to perform a context search on a genetic sequence database comprising loci, each locus having a unique name, one or more annotations, and an ordered text string, the genetic sequence database being stored in one or more database files, wherein said computer program logic comprises:

• read means for enabling the computer to read an ordered string;
• partition means for enabling the computer to partition the ordered string into a plurality of sub-strings each marked either target or context;
• means for enabling the computer to specify one or more context relationships;
• searching means for enabling the computer to search for sub-strings marked target within regions that satisfy the specified context relationships;
• storage means for enabling the computer to store matches found in said searching step;
• means for enabling the computer to mark each sub-string found in said searching step with its associated context;
• means for enabling the computer to create a results hits list comprising an array, wherein each entry of the array comprises an iref number, a type field, and a mark field;
• and
• means for enabling the computer to store a pointer within each mark field that points to the associated context reference entry.

A method for searching a genetic sequence database, the database comprising loci, each locus having a unique name, one or more annotations, and an ordered text string, the database being stored in one or more database files, the method comprising the steps of:

• constructing a file map for the database, said file map comprising the file name of each database file in the database and the number of loci within each file;
• constructing a global index comprising the names of all the loci and a unique ID for each locus;
• building a parsed skeleton file associated with each database file, said parsed skeleton file comprising a plurality of entries, each entry associated with an individual locus, wherein each entry comprises one or more searchable object names, and an offset and length for each searchable object with a locus;
• building an index file associated with each database file, said index file comprising a plurality of entries, each entry associated with an individual locus, wherein each entry comprises an offset into a database file, a length of the locus, an offset into the corresponding parsed skeleton file, and a length of the parsed skeleton file;
• retrieving a unique ID associated with a particular locus of interest;
• consulting the file map to determine the database file that contains the particular locus of interest;
• calculating the offset into said index file associated with said database file;
• reading the index file entry and the parsed skeleton file entry into memory;
• and
• reading a first search query and conducting a first database search.