The Region Search allows you to search for features that overlap a list of genome coordinates. It is found under the Regions tab in the main InterMine header.
Note that you must also select the coordinate system of your regions. Both base coordinate (e.g. BLAST, GFF/GFF3) and interbase coordinate (e.g. UCSC BED, Chado) systems are supported e.g. for a DNA piece GCCATGTA, the position of the ATG in interbase is [3, 6], and in base coordinates is [4, 6]. Users need to explicitly select one. By default, the base coordinate is selected.
Each genomic region needs to take a new line.
The region search provides results in two formats: in a genome browser and as a table (Note; genome browser is not currently configured for FlyMine).
Note that the genome browser will initially display a default region or the last region you looked at. To display one of the regions from your current query click on the region link from the table display. The genome browser will display the Gene track for that region. Further tracks available are shown on the left and can be pulled onto the view.
The table display shows each of your regions in turn. The left hand column shows the region and allows you to download the results for just that region in various formats (tab, csv, gff3, FASTA and BED) or send your results to galaxy. You can also create a list of a specific type of feature. Download and list creation for all regions is found just above the table under the genome browser. The right hand side of the table displays all the features found and their genomic location.
At present, it is not possible to upload genomic regions directly from the results of a InterMine search into the region search. You need to download the regions and reformat them first. This is something we hope to rectify in the future.