Welcome to the OnchoNet Onchocerca volvulus antigens database

This site is designed to help researchers working on filarial parasites access information about all known O. volvulus antigens. You can search the database by key word, by FUNK^* name or get a list of all records of the database.

*FUNK The Filarial Unified Nomenclature Kommittee assigns names for filarial genes. The committee consists of Steven Williams, Mark Blaxter, Alan Scott, Sara Lustigman and David Guiliano. You can use the FUNK link above for more information and guidelines on naming. Please send any questions or comments about FUNK names to Steven Williams at genome@smith.edu or Mark Blaxter at mark.blaxter@ic.ac.uk .

Search engine

About this search engine:

Disclaimer: this engine searches a database that was constructed from all existing GenBank entries for the organism Onchocerca volvulus. Data manipulation being automated, any pre-exisisting error in the NCBI records is passed along to this database. However, if you find some errors, contact me and I will do my best to modify this database to improve its accuracy and performances. For explanations about the contents of this database, see below.

• To search by FUNK names, just enter the FUNK name of the antigen in the first box.
• Searches by function or name can be done using broad terms like "protease", "hormone receptor", "reductase" etc... as well as specific names like "Ov87" or "alt".
• You can combine your query with choosing a given developmental stage (see below for the limitations of this type of search). If you're interested in all proteins for which the cDNA was cloned from a particular developmental stage, just select it, leaving the rest blank.
• The wild card for this search engine is "%".

Full listings:

• A simplified table of all clones in the database is available, that includes for each clone:
  • clickable Genbank ID
  • FUNK name
  • other name(s)
  • direct link to BLAST search

• A full table of all clones in the database with all information is also available.

Explanation of the results:

By using the search engine, or retrieving the full table described above, you will get the following information:

• GenBank accession number: this column provides you with a clickable link to the GenBank report for each entry.
• Tentative FUNK: FUNK names (see note above for more information). These names are tentative, and need to be checked by the filarial research community. In order to make them as acurate and comprehensible as possible, we invite your comments and suggestions.
• Name: this field is extracted from the DEFINITION fields of the GenBank records and gives you the name of the protein product. Several records may correspond to the same antigen, but are still different GenBank entries. These entries often differ, either in their sequence (polymorphism) or in their length, which is indicated by "partial CDS" or "complete CDS" (cDNA Sequence).
• Function: only a minority of the GenBank records report a function for the protein product. The name can often be self-explanatory in terms of the protein function. For all the records where the function was not specified, the name of the protein was used as the function. This might be subject to changes in the future, because many antigens (like the alt proteins for example) currently have an unknown function.
• BLAST: Clicking on this link will directly launch a BLAST search at NCBI, using the program blastx, comparing your sequence to all available sequences (database = "nr").
• ESTblast: Clicking on this link will directly launch a BLAST search at NCBI, using the program blastn, comparing your sequence to all available EST sequences (database = "dbEST").
• Cloning stage: More than half of the Genbank records don't include this information; they are flagged by "not specified" indicated in the cloning stage column. By narrowing down your search of an antigen to a given developmental stage, you unfortunately exclude all those clones and take the risk of missing some antigens even though they are in the database. To perform a search including a cloning stage plus a keyword, it is always recommended to also look at the results you get without selecting the cloning stage.
• Length: length in base pairs of the cDNA encoding the antigen.
• Investigators: Names of the authors who submitted the sequence to GenBank.
• Reference: clickable link that goes directly to the articles published about this antigen in PubMed. This column indicates "NO ENTRY" when the GenBank report of the clone didn't include a direct link to published literature. For more information about those clones, you can click on their Genbank ID and look for references of published articles in the field REFERENCE.