Interpro is a widely used tool for protein annotation in genome sequencing projects, demanding a large amount of computation and representing a huge time-consuming step. We present a strategy to execute programs using databases Pfam, PROSITE and ProDom of Interpro in a distributed environment using a Java-based messaging system. We developed a two-layer scheduling architecture of the distribute...

PPMuSA is a pattern matching program for PROSITE [2] signature patterns against amino acid sequence database. To characterize a group of protein among others, it is important work to find occurrences of a signature in an amino acid sequence of the protein. Such signatures are compiled in databases. The PROSITE is one of the databases of signatures that distinguish members of a protein families ...

We present an efficient algorithm to systematically and automatically identify patterns in protein sequence families. The procedure is based on the Splash deterministic pattern discovery algorithm and on a framework to assess the statistical significance of patterns. We demonstrate its application to the fully automated discovery of patterns in 974 PROSITE families (the complete subset of PROSI...

The papers in the series are intended for internal use and are distributed by the author. Copies may be ordered from the library of Department of Computer Science. Abstract. We consider a problem of learning of unions of pattern languages from positive examples. We consider three diierent classes of patterns-regular patterns, substring patterns and the so called PROSITE patterns. By regular pat...

We present an efŽ cient algorithm to systematically and automatically identify patterns in protein sequence families. The procedure is based on the Splash deterministic pattern discovery algorithm and on a framework to assess the statistical signiŽ cance of patterns. We demonstrate its application to the fully automated discovery of patterns in 974 PROSITE families (the complete subset of PROSI...

Only approximately 51% of the human proteome can be annotated by the standard motif-based recognition systems [1]. These systems, currently aggregated into a single distributed system by InterPro [2], include PFAM, PRINTS, ProSite, ProDom, SMART, and SWIS-PROT+TrEMBL. PFAM consists of hidden Markov models based on hand-curated alignments of protein domains. PRINTS is a repository of protein fin...