FlyBase:Feature Mapper

About Feature Mapper

Feature Mapper allows you to do a search with one or many genes, sequence-based features or genomic regions and returns a wide variety of annotated sequence-based genomic features that overlap or map within the associated genomic region(s). The reported features include gene structure features (including genes, exons, 5’ UTRs, CDSs), aligned evidence (including cDNAs, exon junctions, and peptides), noncoding features (including regulatory regions, insulators, transcription factor binding sites, and RNA editing sites), mapped mutations (including transgenic insertion sites, point mutations, and indels), and RNAi reagents. The search returns lists of features that map to the region(s) of interest in a report that contains the feature type, the feature sequence coordinates, and the feature symbol. Where applicable, the symbol links to the FlyBase report page for that feature. Search results can be saved as a GFF file or exported to a hitlist.

Setting up a Search

Step 1. Enter one or more IDs, symbols, or annotation IDs for FlyBase features (genes, insertions, transcripts, etc.) that have associated sequence coordinates in the “Reference Landmark(s) or Region(s)” box. (N.B. symbol/ID searches are case-senstitive.). Alternatively, enter the sequence coordinates themselves for one or more genomic regions. Any of the following formats for sequence location will work: 2R:13,439,314..13,450,475, 2R:13,439,314-13,450,475, 2R:13439314..13450475, or 2R:13439314-13450475. If you have multiple entries, they can be separated by commas, spaces, or returns.

Step 2. Choose whether you want to query the region of the Landmark itself or just the region upstream or downstream of the landmark (relative to the chromosomal scaffold, not the landmark's orientation) in the "Region type to map" box. If you choose one of the latter options, you will need to specify how many kilobases (kb) upstream or downstream to include in the search by entering a value in the “range” field that appears.

Step 3. Tick the box to "include overlapping (not fully enclosed within query region) features" - that is, tick the box to return features that overlap the ends of the query regions but aren't completely within the bounds of the query region.

Step 4. Choose the species. The default is D. melanogaster but D. pseudoobscura is also an option.

Step 5. Select the tick boxes for the map features you wish to have included in the report and how you’d like the report output organized. The default is to have all the features for each search region listed in order by genomic location. Select the “Group output features by type” tick box to the right of the “Reference Landmark(s) or Region(s)” box to have the output sorted by type and then by genomic location.

Step 6. Click on “Submit Query”

Step 7. The search results can be saved to a GFF file. If you choose to group the output features by type, you additionally have the option to export the results for each feature type to a hitlist.