KoriBlast offers three ways to view and analyse taxonomy data: the Feature Viewer and the Taxonomy Viewer, both of them being located in the Analyse Module; the Global Viewer, introduced in KoriBlast 3.0.

To display the taxonomy data, KoriBlast needs to retrieve it. By defaults, when you submit  a basic search job (just a Blast search), you do not have such data. To get the taxonomy information for the whole set of hits reported in a search result, proceed as follows.

Case 1: using local resources

As you may know, databanks such as SwissProt (for proteins) and Genbank (for nucleotides) usually contains taxonomy information. When you ask KoriBlast to install such as databank from the Databank Manager, it is very important to understand that KoriBlast provides you with a unique feature: it'll inject available classification data (including taxonomy one) directly into the Blast databank. As a result of that feature, when you run a local Blast job against such a locally installed databank, KoriBlast provides you directly with a Blast result containing classification data. This is working, even if you do not select "Featch Feature Data" (see below).

Notice: biological classifications handled this way by KoriBlast include InterPro, PFam, Enzyme, Gene Ontology and NCBI Taxonomy.

Case 2: using public resources

1. From the Search Module. While preparing a search job using public resources (NCBI and EBI), you can request KoriBlast to fetch automatically sequence data as soon as the Blast search is done. To do so, just click on the 'Fetch Sequence data' check box located in the 'Configure Tasks' panel, then submit your job:

When using locally installed databanks, this step is also possible, but key in mind that "Fetching sequence data" really means fetching ALL known sequence data: features table, DB cross-references, classification data, and so on. If you only need to get classification data into your Blast results, read "Case 1" just above.

2. From the Analyse Module. If you forget to fetch the sequence data while preparing a search job (previous step), do not worry. The Analyse Module will help you to do the work. While viewing data in the Hit list, just click on the button located at the bottom of the table: KoriBlast will automatically fetch the sequence data.

Whatever the method used to fetch the sequence data (from the Search Module or from the Analyse one) you have to know that the retrieved information is saved as part of your search job results. Thus, the information remains available across KoriBlast working sessions.

Important notes:

1. By default, KoriBlast always fetch sequence data using the NCBI Entrez  facility. However, it is possible to configure KoriBlast to query your own databases.

2. Retrieving sequence data may appear to be slow when using public resources. It is not: KoriBlast just respects the NCBI/EBI recommandations for the use of their resources. Among others, it is forbidden to query the NCBI faster than one query every 3 seconds to fetch sequence data, and one query every 60 seconds to start a Blast job. In addition, NCBI recommands to wait for the end of one Blast search before sending the next one. Want to work faster ? Configure KoriBlast to work locally, as many of our customers, and you'll see the difference.

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