| How to blast against selected organisms ? |
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Sometimes you could be interested in comparing your sequences only with a selected set of organisms. KoriBlast offers three ways to do this. Case 1: Using the local Blast client The local Blast client enables you to run Blast locally on your system. To do that, you need to install Blast databanks, and this can be done quite easily using the KoriBlast Databank Manager. A major feature of that manager is its capability of handling the NCBI Taxonomy Classification while creating a Blast databank. As a result, the manager enables you to install taxonomy subset of sequences out of larger databank. As an example, consider the "SwissProt_human" databank descriptor available with KoriBlast: you'll see how to prepare taxonomic-based dabatank that meets your needs. You can also read this article. Case 2: Using the NCBI Blast client Using an Entrez Query.
The NCBI allows to provide their BLAST search system with an Entrez
Query (as you can see on the NCBI BLAST form provided by KoriBlast,
there is an Entrez Query field on the Search Parameters panel). This is an expression enabling you to
provide BLAST with additional constraints aim at reducing the search
space.
Let's take an example. Consider you only want to search for sequences related to a particular organism, such as human. Using the Entrez Query entry, just type the following expression: 'Homo sapiens [organism]' (without the quotes). This way, you tell the NCBI BLAST server that it has to compare your query sequence(s) only with human sequences. You can design more complex expressions using the operators OR and AND, such as: 'Homo sapiens [organism] OR Mus musculus [organism]' (without the quotes); OR/AND must be provided using upper case letters. Please note that the Entrez expression does not allow the usage of some characters, such as ( and ). Also, the number of organisms you can provide in the Entrez expression is limited. More on Entrez expressions can be found here . Targetting organism specific sequence banks.
By default KoriBlast is configured to enable the access to the major
sequence databases available at the NCBI. However, the US Institute
provides the scientific community with a wide range of sequence
databases, as explained on this document.
If you are interested in using one of these sequence databases, you just need to declare it to KoriBlast. The procedure is fully explained in the KoriBlast Help manual. Starting from the KoriBlast main frame, click on the large Help and Tutorial button (see bottom left corner of the window). Within the table of content, follow the path: The Configuration Module, Updating the sequence databanks for the NCBI Blast system.
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