3.3 Importing files from public databases

Geneious Prime is able to communicate with a number of public databases hosted by the National Centre for Biotechnology Information (NCBI), as well as the UniProt database. You can access these databases through the web at http://www.ncbi.nlm.nih.gov and http://www.uniprot.org/ respectively. These are all well known and widely used storehouses of molecular biology data - more information on each is given in the sections below.

You can search these databases through Geneious Prime by selecting the NCBI or Uniprot database folders at the bottom of the Sources tree, and entering your search term. Press Enter or the Search button to initiate the search. If you get a connection error, you may need to configure your network connections manually, as described in Section 1.2.5 .

For advanced search options, click the More Options button. This allows you to search for specific terms in specific fields of the Genbank or Uniprot documents, such as specific organisms or author names. By clicking the ’+’ icon you can search in multiple fields at once, and choose to match either “Any” of the fields (if only one of the fields needs to match), or “All” of the fields (if all of the fields must match). For more on advanced search options, see section 4.2 .

If you have a list of known accession numbers that you wish to download, you can enter these in the Search box separated by a comma. For consecutive accessions, enter the first and last numbers separated by a colon, and append [accn] to this. E.g. Entering “AB000001:AB000009[accn]” will download all accessions between AB000001 and AB000009.

The results will appear in the Document table as they are found. The Search button changes to a Stop button while the search is running, and this can be clicked at any time to terminate the search. As the results are downloaded, you will see a small padlock icon in the status bar above the Document Table, which indicates that these items cannot be modified in any way. You must drag the file into a folder in your local database if you wish to retain the file and/or modify it. If you don’t drag the documents from a database search into your local folders the results will be lost when Geneious is closed. For more information on how to move files between folders in your database, see 4.1.1 .

Note: When searching the Genome, Gene or PopSet databases, the documents returned are only summaries. To download the whole genome, select the summary(s) of the genome(s) you would like to download and the click the Download button inside the document view or just above it. Alternatively you can choose Download Documents in the File menu and in the popup menu when document summary is right-clicked (Ctrl+click on Mac OS X). The size of these files is not displayed in the Documents Table. Be aware that whole genomes can be very large and can take a long time to download. You can cancel the download of document summaries by selecting Cancel Downloads from any of the locations mentioned above.

   3.3.1 UniProt
   3.3.2 NCBI (Entrez) databases
   3.3.3 Literature searching