PSSMSearch is a web application to discover novel protein motifs (SLiMs, mORFs, miniMotifs) and PTM sites. PSSMSearch analyses proteomes for regions with significant similarity to a specificity determinant model built from a set of aligned functional peptides. Query peptides can be provided by the users or retrieved from the ELM database. Multiple scoring methods are available to build a position-specific scoring matrix (PSSM) describing the specificity determinant model and users can modify the model to add prior knowledge of specificity determinants through an interactive PSSM heatmap. See the help page for more information.

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"PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants" Izabella Krystkowiak, Jean Manguy, Norman E Davey; Nucleic Acids Research, gky426 doi:10.1093/nar/gky426