exrefPr

exrefPr is a feature of the EMBOSS environment, a software framework for bioinformatics and molecular sequence analysis. The feature is used for the alignment of sequence pairs against a template file in the GenPept or SwissProt format. It has the capability to account for attribute data in the sequence pair, if available.

The feature operates as an extension to the mapper program, allowing users to create mappings that operate on a detail level. Users can provide an exref_filename parameter and an exref_type parameter to enable this feature. exref_filename defines the name of the template sequence file in the required format, and exref_type specifies the format of this file.

exrefPr uses the framework of a contextual template matching algorithm to align sequence pairs against a template of aligned sequences. This approach is designed to maintain a high degree of interaction and responsiveness with the process. The algorithm employed can optimize the match of a pair against a reproducible template sequence alignment by specifying mismatch, swap, and gap gauges which specify penalty rates for differing bases.

The exrefPr feature allows users to apply fine-tuned parameters to optimize alignments according to their specific application requirements. This flexibility combined with response optimizing abilities makes exrefPr a valuable tool for advanced sequence analysis.