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RepSeq-A database of amino acid repeats present in lower eukaryotic pathogens

Lower, R.P.J., Smith, D.F. (orcid.org/0000-0002-8082-5162) and Depledge, D.P. (2007) RepSeq-A database of amino acid repeats present in lower eukaryotic pathogens. Bmc bioinformatics. p. 122. ISSN 1471-2105

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BACKGROUND Amino acid repeat-containing proteins have a broad range of functions and their identification is of relevance to many experimental biologists. In human-infective protozoan parasites (such as the Kinetoplastid and Plasmodium species), they are implicated in immune evasion and have been shown to influence virulence and pathogenicity. RepSeq http://repseq.gugbe.com is a new database of amino acid repeat-containing proteins found in lower eukaryotic pathogens. The RepSeq database is accessed via a web-based application which also provides links to related online tools and databases for further analyses. RESULTS The RepSeq algorithm typically identifies more than 98% of repeat-containing proteins and is capable of identifying both perfect and mismatch repeats. The proportion of proteins that contain repeat elements varies greatly between different families and even species (3 - 35% of the total protein content). The most common motif type is the Sequence Repeat Region (SRR) - a repeated motif containing multiple different amino acid types. Proteins containing Single Amino Acid Repeats (SAARs) and Di-Peptide Repeats (DPRs) typically account for 0.5 - 1.0% of the total protein number. Notable exceptions are P. falciparum and D. discoideum, in which 33.67% and 34.28% respectively of the predicted proteomes consist of repeat-containing proteins. These numbers are due to large insertions of low complexity single and multi-codon repeat regions. CONCLUSION The RepSeq database provides a repository for repeat-containing proteins found in parasitic protozoa. The database allows for both individual and cross-species proteome analyses and also allows users to upload sequences of interest for analysis by the RepSeq algorithm. Identification of repeat-containing proteins provides researchers with a defined subset of proteins which can be analysed by expression profiling and functional characterisation, thereby facilitating study of pathogenicity and virulence factors in the parasitic protozoa. While primarily designed for kinetoplastid work, the RepSeq algorithm and database retain full functionality when used to analyse other species.

Item Type: Article
Copyright, Publisher and Additional Information: © 2007 Tanimoto et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Animals,Databases, Protein,Eukaryota,Information Storage and Retrieval,Internet,Molecular Sequence Data,Proteome,Protozoan Proteins,Repetitive Sequences, Amino Acid,Sequence Analysis, Protein,User-Computer Interface
Institution: The University of York
Academic Units: The University of York > Biology (York)
Depositing User: Sherpa Assistant
Date Deposited: 11 Aug 2007 22:12
Last Modified: 06 Jun 2016 10:00
Published Version: http://dx.doi.org/10.1186/1471-2105-8-122
Status: Published
Refereed: Yes
URI: http://eprints.whiterose.ac.uk/id/eprint/2611

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