ADSP–a new package for computational sequence analysis

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Abstract
A new protein sequence analysis package, ADSP, is described, of which the SOMAP Screen–Oriented Multiple Alignment Procedure forms an integral part. ADSP (Algorithms and Data Structures for Protein sequence analysis) incorporates facilities to generate potent pattern-recognition discriminators and offers four algorithms with which to scan any NBRF format sequence database: the package has been designed, in particular, to interface with the OWL composite sequence database, one of the largest, distributed non-redundant sources of sequence data of its kind. The system incorporates a powerful method for compound feature analysis, which provides the basis for characterizing and predicting the occurrence of complete protein superfamilies and for pinpointing the emergence of related subfamilies. Used iteratively, the approach allows diagnostic performance to be rigorously refined and its efficacy to be assessed both qualitatively and quantitatively, and results in the generation of refined structural or functional features suitable for entry into a database: this compilation of characteristic signatures is distinct from, but complementary to, widely used compendia of pattern templates such as PROSUE.

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