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Tutorial, Quickstarts, New Features, etc.

Run Blast+ Locally with Blast2GO PRO - Step by Step

Blast2GO allows running Blast locally. The blast algorithm will run on the user's computer against a database that is installed locally.
In order to do so, we have to either download a pre-formatted NCBI database or format our own database (see this tutorial until step 3).
Pre-formatted databases can be downloaded directly from the NCBI ftp or via a Perl script provided by the NCBI.
Please follow the steps below to proceed with the download using the Perl script. 
This tutorial will also provide information on how to create an nr subset database to run local Blast against it.

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New Blast2GO Command Line Examples 

(Version 1.4 release date: 01/10/2015)

In the Blast2GO Command Line Manual (PDF) you can now find several practical examples which will help you to get started with Blast2GO over the command line.

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Local Blast2GO Database Installation

(This is now obsolete. The use of the Blast2GO Command Line is recommended for this task.)

This page describes how to create a local installation of the B2G MySQL database and is intended for users with knowledge in MySQL databases and general server administration tasks. If you are not able to follow the steps given here, we recommend you to ask for some help from your system administrator.

After this installation you will end up with a working DB to run Blast2GO with a DB name “b2gdb”, user “blast2go” and a default password “blast4it” being able to run Blast2GO nearly independent from our server. This does NOT include the graph layout generation, GO-Slim reduction and other web-services which are hosted at the Blast2GO or third party server sides which you will still need to access remotely.

B2G users should keep in mind that the B2G-DB schema can be subject of changes as a consequence of the continuous efforts for improving the performance and quality of this annotation framework. We will promptly inform users about any major change, especially concerning the database, through the B2G mail list (http://groups.google.com/group/blast2go) and website. In general, all datasets needed to create a local instance of the Blast2GO database are freely available at different public locations. Since the used resources are not maintained by us, third-party changes can affect these instructions. We will try to keep this as up to date as possible and are happy for receiving any feedback and bug-reports. Thank you.

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How to create a Fasta file database for local Blast and to import XML results successfully into Blast2GO

(Note: This tutorial is based on the NCBI blast binaries released in 2014 and some parameters might have changed since then)

The user can blast their sequences against their own formatted database. One has to be careful when formatting an own database as Blast2GO needs the accession IDs information in order to execute the mapping step correctly.
This tutorial will guide you on how to format your own database from a fasta file and use the correct parameters to run the local blast.

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