ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins

• Published in: Nucleic acids research Vol. 40; no. D1; pp. D394 - D399
• Main Authors: Luo, Hong, Lin, Ke, David, Audrey, Nijveen, Harm, Leunissen, Jack A. M.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2012
• Subjects: alanine; algorithm; annotation resource; codon usage; Databases, Protein; evolution; genomes; Proteins - chemistry; proteomes; Repetitive Sequences, Amino Acid; selection; Sequence Analysis, Protein; sequences; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkr1019

ProRepeat (http://prorepeat.bioinformatics.nl/) is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats' corresponding codons.