PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. Many large proteins have evolved by internal duplication and many internal sequence repeats correspond to functional and structural units. Radar is uses an automatic algorithm, for segmenting your query sequence into repeats, it identifies short composition biased as well as gapped approximate repeats and complex repeat architectures involving many different types of repeats in your query sequence.
Protein search for repeats, using a collection of repeat families
REPRO is able to recognise distant repeats in a single query sequence. The technique relies on a variation of the Smith-Waterman local alignment strategy to find non-overlapping top-scoring local alignments, followed by a graph-based iterative clustering procedure to delineate the repeat set(s) based on consistency of the pairwise top-alignments.
T-REKS is an algorithm for de novo detection and alignment of repeats in sequences based on K-means algorithm. Minimal length of repeat arrays is 9 for true homorepeats and 14 for other repeats with potential biological meaning.
TRUST is a method for ab-initio determination of internal repeats in proteins. The high sensitivity and accuracy of the method is achieved by exploiting the concept of transitivity of alignments.
XSTREAM is a rapid and powerful algorithm for identifying perfect and degenerate tandem repeat motifs in protein (and nucleotide) sequence data. XSTREAM also effectively models the architecture of repetitive domains in tandem repeat proteins and eliminates motif redundancy to identify "fundamental" tandem repeat patterns.