ARKdb can be queried in a number of ways. The main ways of querying are by locus/marker, by published reference or by map. You can also query by clone or library, although these tend to be less well-used areas of the system. Each species database is accessed in the same way. Brief details of the options available are given below. A more detailed guide to the text-based interfaces (locus and reference queries) can be found using the help links in the relevant query pages..
Locus
You can query for a locus based on its symbol, its description (name), chromosome position or marker type. You can also limit the search to markers mapped on a specific mapping population and further refine this search by limiting the search to a particular mapping cross sex. However, you should be aware that it is possible to generate queries that return no markers simply by choosing the incorrect sex in this form, so the option should only be used if you really know what you are doing. You can also partially customise the report format by choosing to display primer details (in which case the query will return symbol, primer sequences and EMBL accession numbers) and sort criteria.
Reference
You can look for specific references by full or partial title, author, journal name or publication year. Alternatively you can use the internal database identifier unique to each reference (accession number).
Map
You can query for maps using either the “advanced” or the “simpler” interface. Maps are selected by species, chromosome and published map name – you can alternatively use your own data to generate maps.
Clone
You can query the database for details of clones used in mapping experiments. The searchable fields are Clone Name, Vector and Cloning Sites.
Library
You can query the database for details of libraries from which clones used in mapping experiments were derived. The searchable fields are Library Name, Vector and Host.
