title: ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins.
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.
authors.affiliation: Laboratory of Bioinformatics, Wageningen University and Research Centre, PO Box 569, 6700 AN Wageningen, Netherlands.
authors.forename: Hong
authors.initials: H
authors.lastname: Luo
authors.forename: Ke
authors.initials: K
authors.lastname: Lin
authors.forename: Audrey
authors.initials: A
authors.lastname: David
authors.forename: Harm
authors.initials: H
authors.lastname: Nijveen
authors.forename: Jack A M
authors.initials: JA
authors.lastname: Leunissen
mesh_terms: D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry*; D020449:Repetitive Sequences, Amino Acid; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
chemical_list: D011506:Proteins
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D272-6
references.pmid: 21059684
references.citation: BMC Bioinformatics. 2007 Oct 11;8:382
references.pmid: 17931424
references.citation: Annu Rev Neurosci. 2007;30:575-621
references.pmid: 17417937
references.citation: Genome Res. 2010 Jun;20(6):755-60
references.pmid: 20056893
references.citation: BMC Bioinformatics. 2006 Jul 07;7:336
references.pmid: 16827924
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D396-403
references.pmid: 18957448
references.citation: Mol Biol Evol. 2006 Nov;23(11):2017-25
references.pmid: 16877497
references.citation: Gene. 2005 Jan 17;345(1):113-8
references.pmid: 15716087
references.citation: Bioinformatics. 2002 May;18(5):672-8
references.pmid: 12050063
references.citation: Nucleic Acids Res. 2005 Jun 10;33(10):3390-400
references.pmid: 15951512
references.citation: J Mol Biol. 2003 Nov 7;333(5):951-64
references.pmid: 14583192
references.citation: BMC Evol Biol. 2008 Mar 27;8:99
references.pmid: 18371205
references.citation: Mol Biol Evol. 1997 Oct;14(10):1042-9
references.pmid: 9335144
references.citation: J Mol Biol. 1999 Oct 15;293(1):151-60
references.pmid: 10512723
references.citation: BMC Bioinformatics. 2005 Aug 03;6:196
references.pmid: 16078990
references.citation: EMBO Rep. 2007 Aug;8(8):737-42
references.pmid: 17668004
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D346-54
references.pmid: 19914934
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D32-6
references.pmid: 18927115
references.citation: Genome. 2006 Aug;49(8):900-5
references.pmid: 17036065
references.citation: Nat Rev Genet. 2005 Oct;6(10):743-55
references.pmid: 16205714
references.citation: Genetics. 2003 Nov;165(3):1613-7
references.pmid: 14668408
references.citation: Genome. 2010 Oct;53(10):753-62
references.pmid: 20962881
references.citation: PLoS Genet. 2009 Mar;5(3):e1000397
references.pmid: 19266028
references.citation: Genetics. 1995 Feb;139(2):921-39
references.pmid: 7713442
references.citation: Curr Opin Struct Biol. 2008 Dec;18(6):756-64
references.pmid: 18952168
references.citation: Mol Biol Evol. 2007 Dec;24(12):2598-609
references.pmid: 17602168
references.citation: BMC Bioinformatics. 2007 Apr 11;8:122
references.pmid: 17428323
references.citation: Hum Mol Genet. 2005 Feb 1;14(3):411-20
references.pmid: 15590697
references.citation: Genome Biol. 2009;10(6):R59
references.pmid: 19486509
references.citation: J Eukaryot Microbiol. 1999 May-Jun;46(3):239-47
references.pmid: 10377985
references.citation: Nat Rev Mol Cell Biol. 2007 Apr;8(4):319-30
references.pmid: 17356578
references.citation: Curr Opin Struct Biol. 2001 Dec;11(6):725-32
references.pmid: 11751054
references.citation: Hum Mol Genet. 2004 Aug 15;13(16):1677-92
references.pmid: 15198988
references.citation: Genome Res. 2004 Apr;14(4):549-54
references.pmid: 15059995
references.citation: Science. 1995 Oct 13;270(5234):293-6
references.pmid: 7569978
references.citation: Genome Res. 2007 Jul;17(7):1118-27
references.pmid: 17567984
references.citation: Genome Res. 2010 Jun;20(6):745-54
references.pmid: 20335526
references.citation: Curr Opin Struct Biol. 1995 Jun;5(3):360-71
references.pmid: 7583634
references.citation: FEBS Lett. 2003 Nov 20;554(3):237-9
references.pmid: 14623072
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W428-34
references.pmid: 19494185
references.citation: Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):333-8
references.pmid: 11782551
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9
references.pmid: 21051339
references.citation: Proteins. 2002 Jul 1;48(1):134-40
references.pmid: 12012345
references.citation: FEBS J. 2010 Aug;277(15):3147-57
references.pmid: 20561057
references.citation: Protein Sci. 2000 Jun;9(6):1203-9
references.pmid: 10892812
references.citation: Trends Genet. 2004 Jan;20(1):51-8
references.pmid: 14698619