Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 414152
Title ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins
Author(s) Luo, H.; Lin, K.; David, A.; Nijveen, H.; Leunissen, J.A.M.
Source Nucleic Acids Research 40 (2012)D1. - ISSN 0305-1048 - p. D394 - D399.
DOI http://dx.doi.org/10.1093/nar/gkr1019
Department(s) Bioinformatics
EPS-4
Publication type Refereed Article in a scientific journal
Publication year 2012
Keyword(s) annotation resource - codon usage - sequences - database - evolution - genomes - selection - alanine - algorithm - proteomes
Abstract 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.
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