FlyBase CytoSearch Query

CytoSearch Help
CytoSearch lists are regional maps of the Drosophila melanogaster genome incorporating both sequence-based and cytology-based map data. 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. Close All Open All
Examples of Search Queries
Category Example Notes Cytolocation 67C, 12A-D, 43, 92A1 Range limit is 2 Mbp, but your browser may timeout even within that range if volume of data is too large. If you encounter a page-not-found error, try narrowing the range or selecting fewer features. Sequence region 2R:2206427..2374251 All features whose directly determined or estimated sequence range overlaps this range will be returned. FlyBase gene ID FBgn0003174 All features whose directly determined or estimated sequence range overlaps the range of this gene will be returned. Gene symbol cnn, alphaTub67C This is a case-insensitive search of valid gene symbols. If the gene symbol is unique without regard to case, all features whose sequence range overlaps the range of this gene will be returned. Use the case-sensitive option for valid symbols that are distinguished from another valid symbol only by case. Gene symbol (case-sensitive) w, W, B, b Use this option for gene symbols that differ from other valid symbols only by case. Gene synonym CG3619, omb, ri This is a case-insensitive search of both valid symbols and synonyms. If your input is not a unique symbol or synonym, a list of options with valid gene symbols will be displayed; use the valid gene symbol with the ‘Gene symbol’ menu option in a new CytoSearch query. Annotation DB ID/ symbol/ synonym CG3757-RA FBtr0088962 AAF59274.2 CG11101-PA FBpp0088036 FBan0011101 Any valid symbol or ID in the annotation database can be used with this option. This is a direct query of the chado PostgreSQL database, primarily intended for debugging use by FlyBase (but knock yourself out).
Other Features
Data on results page can be downloaded as a tab-separated-values file. Sequence range on results page links to GBrowse, which provides a graphical display of annotation and insertions data for that region. Gene, insertion and aberration symbols on results page link to their respective FlyBase reports.
Known Problems
Heterochromatic cytological locations are not supported. Heterochromatic bands will be supported when the heterochromatin sequence data are added to the annotation database. Some features are present in duplicate, under different symbols (the invalid symbol is unlinked). This should be corrected with the next update of the annotation database. Some transgene insertions for which FlyBase has sequence-based map data appear as cytologically mapped insertions. This should be corrected with the next update of the annotation database. Only cytology-based aberration data and estimated cytology for sequence-based aberration data are currently available to CytoSearch. Observed sequence ranges will be added for the DrosDel and Exelixis deficiency collections in the near future. Some genes without annotation data, e.g., Bl, are missing from the dataset. This should be corrected with the next update of the annotation database.