Abstract: Methods and systems for improving computer efficiency by intelligently selecting subsets of possible short tandem repeat (STR) allele combinations for further deconvolution analysis are disclosed. In one embodiment, at each locus, for a currently analyzed contribution ratio scenario of a plurality of contribution ratio scenarios, a processor computes an adjusted evidence profile. For a first, or next, unidentified contributor having a pre-determined highest remaining contribution ratio in the currently analyzed contribution ratio scenario for the plurality of contributors, a processor computes a first range of expected peak heights using at least the pre-determined highest remaining contribution ratio, a selected degradation value, and a peak height ratio distribution. Also disclosed are methods and systems for intelligently estimating the number of contributors to a biological sample.

Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.

Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.

Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.

Abstract: A method for indexing a reference genome is provided. The method includes selecting a reference genome to index, calculating a first minimum index region size, assigning a first position number to a first index region of the reference genome, assigning a second position number to a second index region of the reference genome, and storing the association of the first and second position numbers to index regions in a hash table. The size of the first index region can be greater than or equal to the first minimum index region size. The second index region can overlap with at least one base included in the first index region. The first minimum index region size can be calculated based on the reference genome size. In yet other embodiments of the present teachings, a method for mapping a sequence read to a reference genome is provided wherein a sequence read is compared to the index regions stored in the indexing hash table, and the sequence read is mapped to and aligned against a location on the reference genome.

Abstract: A system is presented with a search panel for specifying search criteria for searching a database of biological information. The search panel uses the extensible markup language (XML) to send search requests to the database. A database graph generation module linked to the biological database generates a database graph representing the database schema. Once the database schema is known, another module creates joins between the database tables in order to most effectively join data from one table to another. An SQL statement incorporating the optimized joins is then used to search the biological database.

Abstract: The present invention relates to systems and methods for formatting and storing data and information collected from diverse biological domains. A uniform method of processing data output from biological sources of information uses an intermediary markup language to reformat the data output and organize the information contained therein for subsequent storage in a data warehouse. A generic loader is implemented and configured to receive data in a transitional format, transpose the data into a database-compatible language and store the data in a data warehouse.

Abstract: A system is presented with a search panel for specifying search criteria for searching a database of biological information. The search panel uses the extensible markup language (XML) to send search requests to the database. A database graph generation module linked to the biological database generates a database graph representing the database schema. Once the database schema is known, another module creates joins between the database tables in order to most effectively join data from one table to another. An SQL statement incorporating the optimized joins is then used to search the biological database.