The Annotate option permits annotating your regions with some of the annotations that are frequently requested by biologists. These annotations are downloaded form the UCSC genome browser, formatted as bed files, and sorted by chromosome and start columns. The bed files are stored in a directory indicating release and genome assembly. Any bed file in the release/assembly directory will be displayed as available annotation. You can choose desired annotations by selecting the overlap and/or neighbor option. By default, only the first overlapping annotation is reported. Select the 'report multiple overlaps' option to see all overlapping annotations.
The regions to be annotated can be supplied as directly pasted text, uploaded from a text file, or read from a URL pointing to a bed file. When submitting a file or a URL upload, you will be automatically returned to the input text area with the content of those files being displayed. To start annotation, click the Submit button. You can use example regions for testing purposes by clicking the example buttons. The input regions you supply in the Annotate page will be remembered also in the Custom or the Distance page. This means that you can annotate your regions consecutively with provided or custom annotations without the need to re-submit your regions.
The annotation results are displayed in a table that can be filtered for terms of interest. All annotations are displayed in a single column. You may want to download the annotation results and paste them into an Excel table where each annotation will be displayed in a separate column. Your result files will be deleted after two hours.
The provided annotations will hardly be sufficient for all purposes. Therefore, custom annotations may be needed. The Custom page allows you to upload bed files to the server and use them for annotating your genomic regions just the same way as the provided annotations. If your annotations are not in the regular bed format, that is chr-start-end-annotation, you may have to adjust the column indices. The first column should have index 1 (not 0). By default, only the first overlapping annotation is reported. Select the 'report multiple overlaps' option to see all overlapping annotations.
The regions to be annotated can be supplied as directly pasted text, uploaded from a text file, or read from a URL pointing to a bed file. When submitting a file or a URL upload, you will be automatically returned to the input text area with the content of those files being displayed. To start annotation, click the Submit button. You can use example regions for testing purposes by clicking the example buttons. The input regions you supply in the Custom page will be remembered also in the Annotate or the Distance page. This means that you can annotate your regions consecutively with provided or custom annotations without the need to re-submit your regions.
You may want to determine the distance of your genomic regions to a given type of annotations. When annotating distances, you need to upload a file with those annotations to the server that contains strand information. The file should be in the format chr-start-end-strand-annotation. If it is not, you have to adjust the column indices. The first column should have index 1 (not 0).
The regions to be annotated can be supplied as directly pasted text, uploaded from a text file, or read from a URL pointing to a bed file. When submitting a file or a URL upload, you will be automatically returned to the input text area with the content of those files being displayed. To start annotation, click the Submit button. You can use example regions for testing purposes by clicking the example buttons. The input regions you supply in the Distance page will be remembered also in the Annotate or the Custom page. This means that you can annotate your regions consecutively with provided, custom, or distance annotations without the need to re-submit your regions.
The results page displays your annotations, allows you to download or filter them, or to view your annotated regions in a Genome Browser.