Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, and locating the one or more keys in an index configured to map a plurality of possible keys to their respective candidate and/or validated locations in a reference.

Abstract: Generating an index includes receiving a reference sequence and applying one or more key patterns to the reference sequence to obtain a plurality of keys in the index. Each of the one or more key patterns is derived based on a corresponding set of oligomer sequence relationships of a plurality of oligomer sequences that are expected to be generated from the reference, and the keys correspond to a plurality of candidate and/or validated locations in the reference sequence.

Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, modifying positions within these keys, and locating the one or more keys in an index configured to map a plurality of candidate and/or validated keys to their respective possible and/or validated locations in a reference.

Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, and locating the one or more keys in an index configured to map a plurality of possible keys to their respective candidate and/or validated locations in a reference.

Abstract: Methods, apparatuses, and systems for identification of junctions (e.g., resulting from large-scale rearrangements) of a sequenced genome with respect to a human genome reference sequence is provided. For example, false positives can be distinguished from actual junctions. Such false positives can result from many sources, including mismapping, chimeric reactions among the DNA of a sample, and problems with the reference genome. As part of the filtering processes, a base pair resolution (or near base pair resolution) of a junction can be provided. In various implementations, junctions can be identified using discordant mate pairs and/or using a statistical analysis of the length distributions of fragments for local regions of the sample genome. Clinically significant junctions can also be identified so that further analysis can be focused on genomic regions that may have more of an impact on the health of a patient.

Abstract: The cost of running a query (having a query range) on a multidimensional database may be estimated using a process factors criteria beyond merely the number of affected records. First, a materialized view of the database may be represented as a container of tuples, sorted by key. Then keys may be stepped through, each key representing a mapping of a combination of tuples from the container. At each step, the process may request the next smallest key in the query range greater than or equal to the key of the current step, which results in the tuple in the database whose key is the smallest, greater than or equal to the requested key, and determine if the resulting is in the query range. The cost of the query may then be estimated as the number of tuples upon which the range check was performed.

Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, modifying positions within these keys, and locating the one or more keys in an index configured to map a plurality of candidate and/or validated keys to their respective possible and/or validated locations in a reference.

Abstract: Embodiments for calling variations in a sample polynucleotide sequence compared to a reference polynucleotide sequence are provided. Aspects of the embodiments include executing an application on at least one computer that locates local areas in the reference polynucleotide sequence where a likelihood exists that one or more bases of the sample polynucleotide sequence are changed from corresponding bases in the reference polynucleotide sequence, where the likelihood is determined at least in part based on mapped mated reads of the sample polynucleotide sequence; generating at least one sequence hypothesis for each of the local areas, and optimizing the at least one sequence hypothesis for at least a portion of the local areas to find one or more optimized sequence hypotheses of high probability for the local areas; and analyzing the optimized sequence hypotheses to identify a series of variation calls in the sample polynucleotide sequence.

Abstract: Generating an index includes receiving a reference sequence and applying one or more key patterns to the reference sequence to obtain a plurality of keys in the index. Each of the one or more key patterns is derived based on a corresponding set of oligomer sequence relationships of a plurality of oligomer sequences that are expected to be generated from the reference, and the keys correspond to a plurality of candidate and/or validated locations in the reference sequence.

Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, and locating the one or more keys in an index configured to map a plurality of possible keys to their respective candidate and/or validated locations in a reference.

Abstract: A method of operating a multi-dimensional database is disclosed. In this method, a multi-dimensional portion of the data is transferred to a multi-dimensional database. A relational portion of the cube is kept in the relational database. When data from the relational portion needs to be accessed, the system produces the SQL queries to obtain data from the relational database.

Abstract: Selection of certain views of a multidimensional database to materialize may be accomplished using an efficient and effective solution. A set of all potential views may be stored in a structure. A path in the structure may then be traversed in an indicated direction through the structure, the path including two or more potential views and beginning at an indicated view. Then two or more immaterialized views in the path may be compared to each other to determine which immaterialized view is the optimum choice for maximizing benefit if selected to be materialized. Then the traversing and comparing may be continually iterated through, each iteration utilizing an indicated direction different than the last, each iteration also utilizing an indicated view set at the optimum choice determined by the last iteration, the iterating continuing until it converges on a single view. That single view may then be selected for materialization.

Abstract: The cost of running a query (having a query range) on a multidimensional database may be estimated using a process factors criteria beyond merely the number of affected records. First, a materialized view of the database may be represented as a container of tuples, sorted by key. Then keys may be stepped through, each key representing a mapping of a combination of tuples from the container. At each step, the process may request the next smallest key in the query range greater than or equal to the key of the current step, which results in the tuple in the database whose key is the smallest, greater than or equal to the requested key, and determine if the resulting is in the query range. The cost of the query may then be estimated as the number of tuples upon which the range check was performed.

Abstract: The cost of running a query (having a query range) on a multidimensional database may be estimated using a process factors criteria beyond merely the number of affected records. First, a materialized view of the database may be represented as a container of tuples, sorted by key. Then keys may be stepped through, each key representing a mapping of a combination of tuples from the container. At each step, the process may request the next smallest key in the query range greater than or equal to the key of the current step, which results in the tuple in the database whose key is the smallest, greater than or equal to the requested key, and determine if the resulting tuple is in the query range. The cost of the query may then be estimated as the number of tuples upon which the range check was performed.

Abstract: A method of operating a multi-dimensional database is disclosed. In this method, a multi-dimensional portion of the data is transferred to a multi-dimensional database. A relational portion of the cube is kept in the relational database. When data from the relational portion needs to be accessed, the system produces the SQL queries to obtain data from the relational database.

Abstract: A method of operating a multi-dimensional database is disclosed. In this method, a multi-dimensional portion of the data is transferred to a multi-dimensional database. A relational portion of the cube is kept in the relational database. When data from the relational portion needs to be accessed, the system produces the SQL queries to obtain data from the relational database.

Abstract: A method of operating a multi-dimensional database is disclosed. In this method, a multi-dimensional portion of the data is transferred to a multi-dimensional database. A relational portion of the cube is kept in the relational database. When data from the relational portion needs to be accessed, the system produces the SQL queries to obtain data from the relational database.