The technology disclosed generates a reference array of variant data for locations that are shared between read results which are to be compared, and generates hashes over a selected pattern length of positions in the reference array to independently produce non-unique window hashes for base patterns in the read results. It then selects for comparison window hashes that occur less than a ceiling number of times and compares the selected window hashes to identify common window hashes between the read results. It then determines a similarity measure for the read results based on the common window hashes.

The technology disclosed generates a reference array of variant data for locations that are shared between read results which are to be compared, and generates hashes over a selected pattern length of positions in the reference array to independently produce non-unique window hashes for base patterns in the read results. It then selects for comparison window hashes that occur less than a ceiling number of times and compares the selected window hashes to identify common window hashes between the read results. It then determines a similarity measure for the read results based on the common window hashes.

Applicants have identified that three critical phenotypic/genetic measures are highly correlated with transition period health and may be used in selection and breeding protocols and/or in combination with traditional breeding and marker assisted selection methods to improve predictability of transition period health. According to the invention genetic evaluations for mastitis, ketosis, and metritis have been found to be highly predictive of overall transition health. The genetic evaluations are produced by directly measuring thousands of clinical cases of mastitis, ketosis, and metritis in ancestors of a particular animal and using this data in selection. Applicant's selection criteria and quickly impact a breeders population by reducing transition cow disease incidence in the initial population and in progeny.

Applicants have identified that three critical phenotypic/genetic measures are highly correlated with transition period health and may be used in selection and breeding protocols and/or in combination with traditional breeding and marker assisted selection methods to improve predictability of transition period health. According to the invention genetic evaluations for mastitis, ketosis, and metritis have been found to be highly predictive of overall transition health. The genetic evaluations are produced by directly measuring thousands of clinical cases of mastitis, ketosis, and metritis in ancestors of a particular animal and using this data in selection. Applicant's selection criteria and quickly impact a breeders population by reducing transition cow disease incidence in the initial population and in progeny.

A computer-implemented method for generating a cover set of biological sequences to detect a group of biological members. The method includes one or more computer processors receiving a request to generate a cover set of k-mers used to detect a first group of biological members that are related via a taxonomic lineage. The method further includes obtaining a plurality of biological sequence data corresponding to biological members of the first group. The method further includes determining a set of k-mers respectively associated with a biological member included within the first group of biological members. The method further includes determining the cover set of k-mers utilized to detect the biological members of the first group by selecting a subset of k-mers from a superset of k-mers associated with the first group of biological members based on preventing false-positive detections of biological members different from the first group of biological members.

A computer-implemented method for generating a cover set of biological sequences to detect a group of biological members. The method includes one or more computer processors receiving a request to generate a cover set of k-mers used to detect a first group of biological members that are related via a taxonomic lineage. The method further includes obtaining a plurality of biological sequence data corresponding to biological members of the first group. The method further includes determining a set of k-mers respectively associated with a biological member included within the first group of biological members. The method further includes determining the cover set of k-mers utilized to detect the biological members of the first group by selecting a subset of k-mers from a superset of k-mers associated with the first group of biological members based on preventing false-positive detections of biological members different from the first group of biological members.

Described are techniques for determining population structure from identity-by-descent (IBD) of individuals. The techniques may be used to predict that an individual belongs to zero, one or more of a number of communities identified within an IBD network. Additional data may be used to annotate the communities with birth location, surname, and ethnicity information. In turn, these data may be used to provide to an individual a prediction of membership to zero, one or more communities, accompanied by a summary of the information annotated to those communities.

Described are techniques for determining population structure from identity-by-descent (IBD) of individuals. The techniques may be used to predict that an individual belongs to zero, one or more of a number of communities identified within an IBD network. Additional data may be used to annotate the communities with birth location, surname, and ethnicity information. In turn, these data may be used to provide to an individual a prediction of membership to zero, one or more communities, accompanied by a summary of the information annotated to those communities.

Displaying an indication of ancestral data is disclosed. An indication that a genetic interval corresponds to a reference interval that has a likelihood of having one or more ancestral origins is received. One or more graphic display parameters are determined based at least in part on the indication. An indication of the one or more ancestral origins is visually displayed using the one or more graphic display parameters.

The present invention includes methods and kits for the diagnosing a neurological disease within primary care settings comprising: obtaining a blood test sample from a subject, measuring IL-7 and TNFα biomarkers in the blood sample, comparing the level of the one or a combination of biomarkers and neurocognitive screening tests with the level of a corresponding one or combination of biomarkers in a normal blood sample and neurocognitive screening tests, and predicting that an increase in the level of the blood test sample in relation to that of the normal blood sample indicates that the subject is likely to have a neurological disease.