1. A method for sequence analysis comprising: storing at least one subject sequence as a relation in a first data object of a relational database; determining an instruction execution plan for an instruction of a query language associated with an operation of the relational database that performs a comparison of at least one relational query sequence within a second data object of the relational database against the at least one relational subject sequence within the first data object, the instruction execution plan having a first part that comprises at least one relational database operation that uses the at least one relational query sequence of the second data object and a third data object of the relational database comprising controls, and the instruction execution plan also having a subsequent part that comprises at least one relational database operation including a JOIN operation, such that the instruction execution plan has multiple parts and includes steps for evaluating data in one or more sequences to determine which of the subject sequence or query sequence is to be specified as an inner table or outer table for the JOIN operation; executing the at least one relational database operation in the first part of the instruction execution plan in a data processing unit; storing a data output result relation of execution of the first part of the instruction execution plan as a database relation in the relational database; using the data output result relation of execution of the first part of the instruction execution plan and the at least one subject sequence of the first data object as at least two data inputs to the at least one relational database operation in the subsequent part of the plan; and executing the at least one relational database operation in the subsequent part of the plan in a data processing unit to complete the comparison.