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.
It might take some time to get the query domains set up but the analysis is worth the wait. The logo and heatmap are very easy to understand and analyze with the provided features.