Abstract: Methods of calling genomic sequence values in complex calling regions are disclosed. Following a preliminary sequence alignment a complex calling region may be identified where no sequence values satisfy preliminary alignment criteria. Potential hypotheses may be formulated for the complex calling region and the probability of each hypothesis representing a correct alignment may be calculated by evaluating the probability of each hypothesis being correct for the reads and the probability of each hypothesis occurring. The hypothesis best satisfying hypothesis selection criteria may be selected. The method may include an evaluation of possible indels in the complex calling region.

Abstract: Methods and systems for simultaneously evaluating biological sequences across multiple population members, and methods and systems for simultaneously calling normal and cancerous biological sequences from a mixed sample containing normal and cancerous material are disclosed. This may be achieved by evaluating the probability of one or more hypothesis being correct for a plurality of population members based on biological sequence information for the population. For related family members, Mendelian inheritance may be integrated into the method. For populations, information from members under evaluation may be used to refine priors to more accurately call population members. Copy number variation, de novo mutations, and phenotypic traits and their genetic explanations may also be accommodated in the methods. Specific systems for implementing the methods are also disclosed.

Abstract: Methods and systems for simultaneously evaluating genomic sequences across multiple population members, and methods and systems for simultaneously calling normal and cancerous genomic sequences from a mixed sample containing normal and cancerous material are disclosed. This may be achieved by evaluating the probability of one or more hypothesis being correct for a plurality of population members based on genomic sequence information for the population. For related family members, Mendelian inheritance may be integrated into the method. For populations, information from members under evaluation may be used to refine priors to more accurately call population members. Copy number variation and de novo mutations may also be accommodated in the methods. Specific systems for implementing the methods are also disclosed.

Abstract: Methods and systems for evaluating genomic sequences are described. The methods include approaches for evaluating the prevalence of genomes in a sample based on the prevalence of segments in the sample, and may additionally rely on the prevalence of segments in reference genomes and an estimated genome population distribution of the sample.

Abstract: A computer implemented method for characterizing one or more sequences by generating index values representing portions of the sequences and finding characterizing index values based on a comparison of the index values. The index values may be obtained by applying one or more mask over each sequence. The modified masks may have associated weightings and index values obtained using modified masks may be retained in the index only if the weightings are above a threshold value. Characterising index values may also be assessed for for their degree of uniqueness. Characterizing indexes may be used for predicting correlation between a sample sequence and one or more reference sequences. Biological monitoring systems utilising the characterizing index values are also disclosed. A biological indicator may be generatgenerated using one or more characterizing index values obtained by the above method and be used to produce an indicator that undergoes a property change in the presence of the one or more sequence.

Abstract: A method of cataloguing a data structure employs the formation of a catalogue data structure which is used to associate data items transformed from data elements present within the data collection with storage addresses of the original transformed data elements. This catalogue data structure may be sorted to facilitate searching through same to detect the presence of search patterns. Such searches may be completed through the formation of a plurality of search queries from a received search pattern sequence where the results of running these search queries may then be subsequently considered in conjunction with a search pattern sequence detection process.