Figure 3

Screenshots of AnnotateGenomicRegions. A) Annotate pane. Here, the user uploads query regions, selects desired release, the genome and embedded annotations of interest, defines if multiple hits shall be displayed, and submits the query. Query regions can be uploaded by pasting them directly, by uploading a file, or by providing a hyperlink to a file in the appropriate format. The format of the query regions can be any of the following position coordinates such as chr1:7577506-7577606 or Chr2:7,577,506-7,577,606 or CHR3:7577506-7,577,606 (case insensitive, with and without thousands separators, colon between chr and start, minus between start and end). Colon and minus characters are not compulsory and space or tabulator characters can be used instead (also called white space characters). Allowing tabulator characters as separators permits pasting query regions directly from a spreadsheet holding chromosome, start, and end positions in separate columns. Note that query regions can be duplicated. These duplications represent alternatively spliced transcripts with identical start and stop positions but with different transcript identifiers. Duplicated regions will be annotated independently from each other as if they were not duplicated. B) Output example. The output lists all the annotations found for each query region. In this example, all RefSeq Symbols for transcription units overlapping the query regions are shown, separated by two forward slash ("/") characters. A hyperlink for downloading the latest results is shown. The hyperlinks corresponding to queries executed earlier are displayed in the Annotation history. Each query region is hyperlinked for display in the UCSC genome browser. Duplicated query regions are listed independently from each other and will display identical annotations. Keeping the duplicates helps keeping the output compatible with the input so that the output can be pasted easily side-by-side to annotations obtained previously. Note that the results page contains a filter function ("annotation results filter"). Typing in the associated text field will filter out all rows that do not contain the typed word in any column. This feature is useful if a researcher is interested in a given gene, for example. Filters can be applied separately to each column by typing in the text fields labeled as "region" or "annotations".