Extracting a subset of a database
After download, it is always possible to select a subset of bacterial genomes and saving the reduced list in a separate file. This can reduce significantly subsequent analysis runtime.
For example, from a collection of bacterial genomes that include multiple representatives of each genus, you can extract a genus specific subset of sequences to a new list:
- Open the downloaded bacterial genomes database.
- Switch to tabular element mode (
).
- Filter towards the desired genus (figure 15.5).
Figure 15.5: The downloaded NCBI bacterial genomes database was filtered for Salmonella data. A subset of 44 out of 2,253 sequences matched this search criterion. - Select all remaining rows.
- Click the Create New Sequence List button.
- Save the subset reference list.