Abstract: Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j)=M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read.

Abstract: Systems and method for annotating variants within a genome can call variants from reads or receive called variants directly and associate the called variants with functional annotations and interpretive annotations. A summary report of the called variants, the associated functional annotations, and the associated interpretive annotations can be generated.

Abstract: Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j)=M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read.

Abstract: Systems and method for annotating variants within a genome can call variants from reads or receive called variants directly and associate the called variants with functional annotations and interpretive annotations. A summary report of the called variants, the associated functional annotations, and the associated interpretive annotations can be generated.

Abstract: Systems and methods for performing a validated analysis can include access to first and second versions of an analysis engine. The first version of the analysis engine can be used to perform a previously validated analysis. After the second version is made available, the first version can be continued to be used while the second version undergoes validation. The user can initiate a migration from the first version to the second version when the validation is complete. Access to both versions can be maintained for a period of time to allow users to migrate on their own schedule, and a common login interface can direct the user to a default version or allow the user to select an alternate version.

Abstract: Systems and method for annotating variants within a genome can call variants from reads or receive called variants directly and associate the called variants with functional annotations and interpretive annotations. A summary report of the called variants, the associated functional annotations, and the associated interpretive annotations can be generated.

Abstract: Systems and methods for performing a validated analysis can include access to first and second versions of an analysis engine. The first version of the analysis engine can be used to perform a previously validated analysis. After the second version is made available, the first version can be continued to be used while the second version undergoes validation. The user can initiate a migration from the first version to the second version when the validation is complete. Access to both versions can be maintained for a period of time to allow users to migrate on their own schedule, and a common login interface can direct the user to a default version or allow the user to select an alternate version.

Abstract: Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j)=M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read.

Abstract: An automated system for evaluating biological samples which includes a centralized registry that contains protocols and configuration information for both instruments and analysis applications. The registry provides for improved automation of biological process runs using an autoanalysis applications manager component or daemon, which accesses and transmits the appropriate protocol and configuration information to selected instruments and/or applications. This information is used to instruct data capture by the biological instruments and direct the analysis of the data by the analysis applications.

Abstract: An automated system for evaluating biological samples which includes a centralized registry that contains protocols and configuration information for both instruments and analysis applications. The registry provides for improved automation of biological process runs using an autoanalysis applications manager component or daemon, which accesses and transmits the appropriate protocol and configuration information to selected instruments and/or applications. This information is used to instruct data capture by the biological instruments and direct the analysis of the data by the analysis applications.

Abstract: An automated system for evaluating biological samples which includes a centralized registry that contains protocols and configuration information for both instruments and analysis applications. The registry provides for improved automation of biological process runs using an autoanalysis applications manager component or daemon, which accesses and transmits the appropriate protocol and configuration information to selected instruments and/or applications. This information is used to instruct data capture by the biological instruments and direct the analysis of the data by the analysis applications.

Abstract: Methods and software for associating mobility probes with target macromolecules are discussed. By encoding the identities of macromolecules of interest with a universal set of tag portions complementary to a universal set of mobility probes, reactions varying in their input starting material may be identified using the same universal set of mobility probes. This allows the universal collection of mobility probes to be used in a target macromolecule-independent manner. Software is used to decode the associations between the mobility probes and a given target macromolecular identity.

Abstract: The present teachings relate to management of storage space for embedded databases in software systems. In various embodiments, the present teachings enable a user to (i) pre-allocate disk space for an embedded database; and/or, (ii) change the disk space allocated to an application's embedded database. The former can be effected, in various embodiments, when the software application is installed, and the latter when the software is running. One or both of these tasks can be accomplished via a graphical user interface (GUI) permitting and facilitating user interaction.

Abstract: An automated system for evaluating biological samples which includes a centralized registry that contains protocols and configuration information for both instruments and analysis applications. The registry provides for improved automation of biological process runs using an autoanalysis applications manager component or daemon, which accesses and transmits the appropriate protocol and configuration information to selected instruments and/or applications. This information is used to instruct data capture by the biological instruments and direct the analysis of the data by the analysis applications.

Abstract: Methods, systems, and articles of manufacture consistent with the present invention are provided for making allele calls. In certain embodiments, allele calling is accomplished by providing a committee machine that receives calls from several allele calling algorithms. By receiving calls from multiple allele calling algorithms, the committee machine makes calls containing a high level of confidence over a variety of conditions. Certain embodiments provide methods employing at least two algorithms and at least two quality values for allele calling. Unique individual algorithms for allele calling are also provided.