ProtVirDB: a database of protozoan virulent proteins.
ABSTRACT ProtVirDB is a comprehensive and user-friendly web-based knowledgebase of virulent proteins belonging to protozoan species. The database will facilitate research and provide an integrated platform for comparative studies of virulent proteins in different parasitic protozoans and organize them under a unifying classification schema with functional categories. Remarkably, one-third of the protein sequences in the database showed presence of either mono- or hetero-repeats, or both concomitantly--hence reiterating the importance of repeats in parasite virulence mechanisms. A number of useful bioinformatics tools including BLAST and tools for phylogenetic analysis are integrated with the database. With the rapidly burgeoning interest in the pathogenesis mechanisms of protozoans and ongoing genome sequencing projects, we anticipate that the database will be a useful tool for the research community. AVAILABILITY: http://bioinfo.icgeb.res.in/protvirdb. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
- SourceAvailable from: fiocruz.brTrends in Genetics 07/2000; 16(6):276-7. · 9.77 Impact Factor
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ABSTRACT: 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. 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. 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.BMC Bioinformatics 01/2007; 8:122. · 3.02 Impact Factor
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ABSTRACT: We have written a fast implementation of the popular Neighbor-Joining tree building algorithm. QuickTree allows the reconstruction of phylogenies for very large protein families (including the largest Pfam alignment containing 27000 HIV GP120 glycoprotein sequences) that would be infeasible using other popular methods.Bioinformatics 12/2002; 18(11):1546-7. · 5.32 Impact Factor