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

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Luo, Hong ^a,b   Lin, Ke ^a   David, Audrey ^a   Nijveen, Harm ^a,b,c   Leunissen, Jack A M ^a,b,c  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b NETHERLANDS BIOINFORMATICS CENTRE   (Netherlands)

^c Netherlands Consortium for Systems Biology NCSB   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

AMINO ACID SEQUENCE; ARTICLE; CODON USAGE; COMPUTER INTERFACE; DNA BASE COMPOSITION; INFORMATION RETRIEVAL; INFORMATION SERVICE; INFORMATION STORAGE; INTERNET; PRIORITY JOURNAL; PROREPEAT DATABASE; PROTEIN DATABASE; TANDEM REPEAT; UNIPROT;

DATABASES, PROTEIN; PROTEINS; REPETITIVE SEQUENCES, AMINO ACID; SEQUENCE ANALYSIS, PROTEIN; USER-COMPUTER INTERFACE;

EID: 84862215448     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1019     Document Type: Article

References (47)

1. Orr,H.T. and Zoghbi,H.Y. (2007) Trinucleotide repeat disorders. Annu. Rev. Neurosci., 30, 575-621. (Pubitemid 47218768)
2. Buchanan,G., Yang,M., Cheong,A., Harris,J.M., Irvine,R.A., Lambert,P.F., Moore,N.L., Raynor,M., Neufing,P.J., Coetzee,G.A. et al. (2004) Structural and functional consequences of glutamine tract variation in the androgen receptor. Hum. Mol. Genet., 13, 1677-1692. (Pubitemid 39173438)
3. Brown,L., Paraso,M., Arkell,R. and Brown,S. (2005) In vitro analysis of partial loss-of-function ZIC2 mutations in holoprosencephaly: alanine tract expansion modulates DNA binding and transactivation. Hum. Mol. Genet., 14, 411-420. (Pubitemid 40220658)
4. Brown,L.Y. and Brown,S.A. (2004) Alanine tracts: the expanding story of human illness and trinucleotide repeats. Trends Genet., 20, 51-58. (Pubitemid 38032820)
5. Gatchel,J.R. and Zoghbi,H.Y. (2005) Diseases of unstable repeat expansion: mechanisms and common principles. Nat. Rev. Genet., 6, 743-755. (Pubitemid 41400832)
6. Labaj,P.P., Leparc,G.G., Bardet,A.F., Kreil,G. and Kreil,D.P. (2010) Single amino acid repeats in signal peptides. FEBS J., 277, 3147-3157.
7. Hancock,J.M. and Simon,M. (2005) Simple sequence repeats in proteins and their significance for network evolution. Gene, 345, 113-118. (Pubitemid 40208507)
8. Salichs,E., Ledda,A., Mularoni,L., Alba,M.M. and de la Luna,S. (2009) Genome-wide analysis of histidine repeats reveals their role in the localization of human proteins to the nuclear speckles compartment. PLoS Genet., 5, e1000397.
9. Kobe,B. and Kajava,A.V. (2001) The leucine-rich repeat as a protein recognition motif. Curr. Opin. Struct.l Biol., 11, 725-732. (Pubitemid 34076634)
10. Miller,M.K., Bang,M.L., Witt,C.C., Labeit,D., Trombitas,C., Watanabe,K., Granzier,H., McElhinny,A.S., Gregorio,C.C. and Labeit,S. (2003) The muscle ankyrin repeat proteins: CARP, ankrd2/Arpp and DARP as a family of titin filament-based stress response molecules. J. Mol. Biol., 333, 951-964. (Pubitemid 37324498)
11. Labeit,S. and Kolmerer,B. (1995) Titins: giant proteins in charge of muscle ultrastructure and elasticity. Science, 270, 293-296.
12. Callis,J., Carpenter,T., Sun,C.W. and Vierstra,R.D. (1995) Structure and evolution of genes encoding polyubiquitin and ubiquitin-like proteins in Arabidopsis thaliana ecotype Columbia. Genetics, 139, 921-939.
13. Simon,M. and Hancock,J.M. (2009) Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. Genome Biol., 10, R59.
14. Karlin,S., Brocchieri,L., Bergman,A., Mrazek,J. and Gentles,A.J. (2002) Amino acid runs in eukaryotic proteomes and disease associations. Proc. Natl Acad. Sci. USA, 99, 333-338. (Pubitemid 34060363)
15. Monsellier,E. and Chiti,F. (2007) Prevention of amyloid-like aggregation as a driving force of protein evolution. EMBO Rep., 8, 737-742. (Pubitemid 47202452)
16. Han,J.H., Batey,S., Nickson,A.A., Teichmann,S.A. and Clarke,J. (2007) The folding and evolution of multidomain proteins. Nat. Rev. Mol. Cell. Biol., 8, 319-330. (Pubitemid 46474660)
17. Depledge,D.P. and Dalby,A.R. (2005) COPASAAR-a database for proteomic analysis of single amino acid repeats. BMC Bioinformatics, 6, 196.
18. Depledge,D.P., Lower,R.P. and Smith,D.F. (2007) RepSeq-a database of amino acid repeats present in lower eukaryotic pathogens. BMC Bioinformatics, 8, 122.
19. Kalita,M.K., Ramasamy,G., Duraisamy,S., Chauhan,V.S. and Gupta,D. (2006) ProtRepeatsDB: a database of amino acid repeats in genomes. BMC Bioinformatics, 7, 336.
20. Katti,M.V., Sami-Subbu,R., Ranjekar,P.K. and Gupta,V.S. (2000) Amino acid repeat patterns in protein sequences: their diversity and structural-functional implications. Protein Sci., 9, 1203-1209. (Pubitemid 30419154)
21. Faux,N.G., Huttley,G.A., Mahmood,K., Webb,G.I., de la Banda,M.G. and Whisstock,J.C. (2007) RCPdb: an evolutionary classification and codon usage database for repeat-containing proteins. Genome Res., 17, 1118-1127. (Pubitemid 47026359)
22. Robertson,A.L., Bate,M.A., Androulakis,S.G., Bottomley,S.P. and Buckle,A.M. (2011) PolyQ: a database describing the sequence and domain context of polyglutamine repeats in proteins. Nucleic Acids Res., 39, D272-D276.
23. The UniProt Consortium. (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res., 39, D214-D219.
24. Pruitt,K.D., Tatusova,T., Klimke,W. and Maglott,D.R. (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res., 37, D32-D36.
25. Gusfield,D. and Stoye,J. (2004) Linear time algorithms for finding and representing all the tandem repeats in a string. J. Comput. Syst. Sci., 69, 525-546.
26. Newman,A.M. and Cooper,J.B. (2007) XSTREAM: a practical algorithm for identification and architecture modeling of tandem repeats in protein sequences. BMC Bioinformatics, 8, 382.
27. Alba,M.M., Laskowski,R.A. and Hancock,J.M. (2002) Detecting cryptically simple protein sequences using the SIMPLE algorithm. Bioinformatics, 18, 672-678. (Pubitemid 34679113)
28. Karlin,S. (1995) Statistical significance of sequence patterns in proteins. Curr. Opin. Struct. Biol., 5, 360-371.
29. Liolios,K., Chen,I.M., Mavromatis,K., Tavernarakis,N., Hugenholtz,P., Markowitz,V.M. and Kyrpides,N.C. (2010) The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res., 38, D346-D354.
30. Barrell,D., Dimmer,E., Huntley,R.P., Binns,D., O'Donovan,C. and Apweiler,R. (2009) The GOA database in 2009-an integrated Gene Ontology Annotation resource. Nucleic Acids Res., 37, D396-D403.
31. Marcotte,E.M., Pellegrini,M., Yeates,T.O. and Eisenberg,D. (1999) A census of protein repeats. J. Mol. Biol., 293, 151-160. (Pubitemid 29494877)
32. Lovell,S.C. (2003) Are non-functional, unfolded proteins ('junk proteins') common in the genome? FEBS Lett., 554, 237-239.
33. Huntley,M.A. and Golding,G.B. (2002) Simple sequences are rare in the Protein Data Bank. Proteins, 48, 134-140. (Pubitemid 34595056)
34. Haerty,W. and Golding,G.B. (2010) Low-complexity sequences and single amino acid repeats: not just 'junk' peptide sequences. Genome, 53, 753-762.
35. Dunker,A.K., Silman,I., Uversky,V.N. and Sussman,J.L. (2008) Function and structure of inherently disordered proteins. Curr. Opin. Struct. Biol., 18, 756-764.
36. Haerty,W. and Golding,G.B. (2010) Genome-wide evidence for selection acting on single amino acid repeats. Genome Res., 20, 755-760.
37. Mularoni,L., Ledda,A., Toll-Riera,M. and Alba,M.M. (2010) Natural selection drives the accumulation of amino acid tandem repeats in human proteins. Genome Res., 20, 745-754.
38. Huntley,M.A. and Golding,G.B. (2006) Selection and slippage creating serine homopolymers. Mol. Biol. Evol., 23, 2017-2025. (Pubitemid 44536811)
39. Huntley,M.A. and Clark,A.G. (2007) Evolutionary analysis of amino acid repeats across the genomes of 12 Drosophila species. Mol. Biol. Evol., 24, 2598-2609.
40. Zhang,L., Yu,S., Cao,Y., Wang,J., Zuo,K., Qin,J. and Tang,K. (2006) Distributional gradient of amino acid repeats in plant proteins. Genome, 49, 900-905. (Pubitemid 44902210)
41. Nakachi,Y., Hayakawa,T., Oota,H., Sumiyama,K., Wang,L. and Ueda,S. (1997) Nucleotide compositional constraints on genomes generate alanine-, glycine-, and proline-rich structures in transcription factors. Mol. Biol. Evol., 14, 1042-1049. (Pubitemid 27419240)
42. Alba,M.M. and Guigo,R. (2004) Comparative analysis of amino acid repeats in rodents and humans. Genome Res., 14, 549-554. (Pubitemid 38500225)
43. Cocquet,J., De Baere,E., Caburet,S. and Veitia,R.A. (2003) Compositional Biases and Polyalanine Runs in Humans. Genetics, 165, 1613-1617. (Pubitemid 38020275)
44. Pozzoli,U., Menozzi,G., Fumagalli,M., Cereda,M., Comi,G.P., Cagliani,R., Bresolin,N. and Sironi,M. (2008) Both selective and neutral processes drive GC content evolution in the human genome. BMC Evol. Biol., 8, 99.
45. Wuitschick,J.D. and Karrer,K.M. (1999) Analysis of genomic G +C content, codon usage, initiator codon context and translation termination sites in Tetrahymena thermophila. J. Eukaryot. Microbiol., 46, 239-247. (Pubitemid 29284924)
46. Brocchieri,L. and Karlin,S. (2005) Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res., 33, 3390-3400. (Pubitemid 41199547)
47. Kuzniar,A., Lin,K., He,Y., Nijveen,H., Pongor,S. and Leunissen,J.A. (2009) ProGMap: an integrated annotation resource for protein orthology. Nucleic Acids Res., 37, W428-W434.