About Repeats Search

   Amino acid repeats are sequences which are repeating atleast twice within the protein sequence. They can range from very small to significant fraction, functionally neutral or significant in different proteins. Amino acid repeats most often contribute to polymorphism in proteins, implying no significant function. Many studies have shown the functional significance of repeats in certain proteins like role of glutamine, alanine, proline and glycine homoruns (reiteration of one amino acid) in protein-protein interaction and/or regulation of transcription, neurodegenerative diseases.

   Rapid sequencing of proteomes of several organisms provides a unique opportunity to perform comparative studies of amino acid repeats in organisms. Such studies can give us unprecedented opportunity to perform large scale studies of genome wide patterns and evolution of the repeats.Recently, the role of polyalanine tracts in congenital malformations, skeletal dysplasia and nervous system anomalies, glycine-proline repeats, polar zippers, prion like glutamine/asparagine-rich stretches and list of other repeats was elucidated.The role of repeats in antigenic variation and immune evasion mechanisms by pathogens is a well known phenomenon which has been proposed to work as per 'smokescreen theory'.

    ProtRepeatsDB is a relational database of direct repeats, access to which is designed as a resource and collection of tools for detection and cross species comparisons of amino acid repeats. It is comprehensive catalogue of protein repeats in 141 organisms from archea, eubacteria, and eukaryotic origin. Repeat finding is an arduous task, all the repeat finding strategies have some limitation or the other; this is primarily due to the ambiguous definition and diversity of repeats. Most of the available repeat finders are based on the algorithms which are variations of Smith-Waterman local alignment (using substitution matrices). To find all possible kinds of repeats, namely; exact, substituted, tandem, homo repeats and scattered hetero repeats, the available programs are not suited to meet the needs. Our perl script DIREP has been designed which detects all the direct repeats except substituted ones.