Importing sequences/features from websites such as ENSEMBL or UCSC’s Genome Browser

Many Genome Browsers/databases allow you to browse and view genomes, or a specific gene/region, with a high degree of detail. For example ENSEMBL and the UCSC Genome Browser. However, many times you want to work with that data on your own Mac. As usual the easiest way to exchange sequence data is using the Genbank format. This stores ALL biological annotation about a sequence and is of course fully supported by MacVector.

However, a better way is to “refresh” your own sequence with the latest current data, using MacVector’s IMPORT FEATURES tool. This will use annotation, using a format such as GFT, GFF or BED, from a genome browser and import to an existing sequence. Very useful for keeping your own sequence, current with known and published annotation about that sequence.

The following example uses ENSEMBL, but the general workflow applies to other Genome Browsers:

  • Choose the region of interest
  • To import a Genbank file:

  • in OUTPUT choose GENBANK and click NEXT
  • Choose the TEXT format.
  • Switch to MacVector and use FILE |NEW FROM CLIPBOARD.
  • To import annotation using IMPORT FEATURES:

  • in OUTPUT choose GFF3 (or BED/GFT) and click NEXT
  • Choose the TEXT format.
  • Save the file.
  • Switch to MacVector and use FILE | IMPORT FEATURES.
  • Read more about importing annotation in general and importing from ENSEMBL.

    This entry was posted in Techniques, Tips and tagged , , . Bookmark the permalink. Both comments and trackbacks are currently closed.