ProtVirDB: Tutorial

Important points

The ProtVirDB database contains a collection of experimentally verified virulent proteins from twelve parasitic protozoans. Some of these proteins have been only identified by a functional assay and do not have their sequences available as yet. Against such proteins, the sequence is N.i., where N.i. stands for 'Not identified'. The pI and molecular weight for these is given as zero.There are 29 such proteins.

The total number of unique proteins in the database is 345, however the total number of proteins is 1775, because there are many polymorphic proteins like trans-sialidase, cruzipain etc.

Query page

The query page gives you the option to search the database in four different ways:

You may search for the virulent proteins in one or more organisms of your choice within one or more of the given eight categories.
You may search for a specific keyword and optionally filter it by the organism.
If you know the accession number of a protein within the database, you may give the required accession number.
You may search for all proteins with molecular weights in a certain range and optionally filter it by organism.

Tools

The tools include the ViroBlast tool (developed by Deng et. al., 2007, ViroBlast) which offers the additional advantage of parsing the results with the cut-off E-values and percent identity after the normal blast procedure.
The ClustalW (Thompson et. al.,1994) and Muscle (Edgar et. al., 2004) tools along with the Jalview editor facilitate the easy visualisation and editing of multiple alignment of input sequences.
The phylogenetic program quick-tree (Howe et. al., 2002) allows fast implementation of the neighbour-joining algorithm to allow phylogenetic analysis.
The antigenic program from the EMBOSS (Rice et. al., 2000) package is to find out the immunologically most relevant regions of a protein sequence.
The ProbeMotiF is a novel tool that allows the user to search for a motif within a specific category of the ProtVirDB database or a sequence set of his choice. Since this tool is based on a perl script it also allows flexibility in the given motif.
As for example, the following motif [KLM]HF{3}NH means either K or L or M followed by H and three F's and then N and H.

Be careful in providing the right input format to these programs. Help for specific parameters for each program is provided in relevant cases. Also conform to the limits given to file upload size given therein, if you wish to analyze files larger than the specified size you may write to the The ProtVirDB Team.

Links

The Links page provides links to several programs for antigenicity and epitope prediction which are relevant to this collection of proteins which represent potential vaccines.


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