FlyBase:CytoSearch Help

About CytoSearch

CytoSearch query will return lists of all the mapped genes, transgene insertions, and aberrations that are within, overlap or include the query region. The query returns features mapped both at the cytological and at the sequence level. Each hit includes the cytology, the observed (in green) or estimated (in red) sequence coordinates, and the symbol of the mapped feature as well as available stocks.

For CytoSearch searches, sequence-based data trumps cytology when both are available, cytology trumps meiotic data when both are available, and estimated cytology is used when only meiotic data are available. The FlyBase correspondence tables for cytological and sequence level maps are used to estimate cytology from sequence range and sequence range from cytology, for both the underlying data and the query input.

Setting up a Search

Choose the type of search value you would like to use (cytological location, sequence coordinates, gene or annotation symbol or ID), from the dropdown menu and enter the value in the box. Select the classes of mapped entities you want returned in the search. The default search will list all features in the region sorted by cytological location. You can choose to group the results by type and to return only features with available stocks. Click on the “Submit Query” button.

Other Features

The number of features of each type are displayed across the top of the results page.

Sequence range on results page links to GBrowse, which provides a graphical display of annotation, insertion, and aberration data for that region.

Gene, insertion, aberration, and stock symbols on the results page link to their respective FlyBase reports. If multiple stocks are available, the number of stocks is shown, which links to a hit list of relevant stocks.

Data on results page can be exported to Batch Download or QueryBuilder by clicking on the blue “Export Hits” box in the upper right corner. If you wish to export the results for one data type, choose the option to sort the CytoSearch results by type when you run the search, then choose the “Export to hitlist” option for your data type or interest. You will then have access to the many options available from the hit list pages. These are described on the [hitlist help page] (link).