Figure 3: Screenshot of the web form to define parameters for retrieval of sequences from genome project (annotated) VSGs in FASTA format or as a temporary database against which to BLAST a query sequence. For non-genome project (unannotated) VSGs, only the type of sequence and the organism need to be specified.

Mentions: • VSG sequence retrieval – The user is allowed to choose from several parameters and retrieve sequence data from the source files in the popular FASTA format [26]. For the annotated VSGs, these parameters include the type of sequence (DNA or protein), one or all chromosomes or contigs, the type of VSG (functional, pseudogene, etc.), the part of the VSG (full-length VSG, N-terminal domain, etc.), and the types of N- and C-terminal domains. Selection for N-terminal domains allows retrieval of the whole set of putative α-helical coiled coil sequences, or subsets thereof. For the VSGs not from the genome project, only the full sequence is returned. The user can select sequences from this set on the basis of species and strain/VSG repertoire, and can choose linkage to other databases. Figure 3 shows a screenshot of the web form where the user can select parameters.

Marcello L, Menon S, Ward P, Wilkes JM, Jones NG, Carrington M, Barry JD - BMC Bioinformatics (2007)

Bottom Line: Trypanosomes are coated with a variant surface glycoprotein (VSG) that is so densely packed that it physically protects underlying proteins from effectors of the host immune system.The database can be queried in various ways.Retrieved sequences can be stored as a temporary database for BLAST querying, reports from which include hyperlinks to the genome project database (GeneDB) CDS Info and to individual VSGdb pages for each VSG, containing annotation and sequence data.

Affiliation: Wellcome Centre for Molecular Parasitology, University of Glasgow, Glasgow Biomedical Research Centre, Glasgow, UK. l.marcello.1@research.gla.ac.uk <l.marcello.1@research.gla.ac.uk>

Abstract: Trypanosomes are coated with a variant surface glycoprotein (VSG) that is so densely packed that it physically protects underlying proteins from effectors of the host immune system. Periodically cells expressing a distinct VSG arise in a population and thereby evade immunity. The main structural feature of VSGs are two long alpha-helices that form a coiled coil, and sets of relatively unstructured loops that are distal to the plasma membrane and contain most or all of the protective epitopes. The primary structure of different VSGs is highly variable, typically displaying only ~20% identity with each other. The genome has nearly 2000 VSG genes, which are located in subtelomeres. Only one VSG gene is expressed at a time, and switching between VSGs primarily involves gene conversion events. The archive of silent VSGs undergoes diversifying evolution rapidly, also involving gene conversion. The VSG family is a paradigm for alpha helical coiled coil structures, epitope variation and GPI-anchor signals. At the DNA level, the genes are a paradigm for diversifying evolutionary processes and for the role of subtelomeres and recombination mechanisms in generation of diversity in multigene families. To enable ready availability of VSG sequences for addressing these general questions, and trypanosome-specific questions, we have created VSGdb, a database of all known sequences.VSGdb contains fully annotated VSG sequences from the genome sequencing project, with which it shares all identifiers and annotation, and other available sequences. The database can be queried in various ways. Sequence retrieval, in FASTA format, can deliver protein or nucleotide sequence filtered by chromosomes or contigs, gene type (functional, pseudogene, etc.), domain and domain sequence family. Retrieved sequences can be stored as a temporary database for BLAST querying, reports from which include hyperlinks to the genome project database (GeneDB) CDS Info and to individual VSGdb pages for each VSG, containing annotation and sequence data. Queries (text search) with specific annotation terms yield a list of relevant VSGs, displayed as identifiers leading again to individual VSG web pages.VSGdb http://www.vsgdb.org/ is a freely available, web-based platform enabling easy retrieval, via various filters, of sets of VSGs that will enable detailed analysis of a number of general and trypanosome-specific questions, regarding protein structure potential, epitope variability, sequence evolution and recombination events.