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Tips, Tricks and Video Tutorial

Mini-tutorials for common use-cases and to address frequently asked questions FAQs

How to Set Maximum Memory for Blast2GO

OmicsBox/Blast2GO automatically reserves up to 80% of the available system memory (i.e. RAM), which is fine in most cases. However, sometimes and especially on Linux, this can lead to excessive swapping and will slow down Blast2GO. Follow this guide to manually change the maximum amount of memory Blast2GO will be allowed to use.

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Some parts of the application are not working (Show Blast Results, Welcome Part, Create Workflow) running Linux system.

This applies to OmicsBox or Blast2GO 5. You need to install some packages depending on your distribution in order to make some parts work. For Ubuntu/Debian: apt-get install libxss1 libgconf-2-4 For Fedora: yum install libXScrnSaver libXScrnSaver.i686 GConf2 For CentOS: yum install libXScrnSaver GConf2 For more information on Show Blast Results or create Workflows, please have a look at the OmicsBox

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How to run Blast2GO installer in Linux systems?

To the Blast2GO installer in Linux systems follow the next steps: 0. Open a terminal in the folder where you have downloaded the installer. 1. Unzip the file: tar -xvf Blast2GO_unix_X_X_XX.zip 2. Make sure the .sh file has execution permissions: chmod +x Blast2GO_unix_X_X_XX.sh 3. Execute the .sh file: ./Blast2GO_unix_X_X_XX.sh An installation wizard should open. Just follow the instructions on the

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How to install OmicsBox on a shared workstation with multiple user access?

This article describes how you can get OmicsBox installed in a central computer where multiple users have access and what you need to configure so that it doesn’t ask for the License key for every new user and the updates are performed centrally. 0.0. You need a Unix user group that common to all the users that will execute OmicsBox.

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Error when running LocalBlast “NCBI Binaries C++ Exception”.

The error looks like: “Critical: (110.6) CNcbiRegistry: Syntax error in system-wide configuration file: NCBI C++ Exception: “……….\src\corelib\ncbireg.cpp”, line 660: Error: ncbi::IRWRegistry ::x_Read() – Badly placed ‘\’ in the registry value: ‘ROOT=J:\nASNLOAD=J:\BioEdi t\tables\nDATA=J:\BioEdit\tables\’ (m_Pos = 4)Error: NCBI C++ Exception: “……….\src\corelib\ncbireg.cpp”, line 660: Error: ncbi::IRWRegistry ::x_Read() – Badly placed ‘\’ in the registry value: ‘ROOT=J:\nASNLOAD=J:\BioEdi t\tables\nDATA=J:\BioEdit\tables\’ (m_Pos = 4)” This error is

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Reformat Uniprot/Swissprot Species Distribution

Reformat/adapt Blast XML results against a custom UniProt sequence database to generate a species distribution chart Problem: Empty species distribution chart Solution: Reformat your SwissProt/UniProt blast XML results The species distribution chart is a good way to visualise the species found for all blast hits for a given dataset. It is possible to generate this chart with OmicsBox from the toolbar: functional

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Select .pal files to Run LocalBlast

Run Local Blast within OmicsBox

OmicsBox 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

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Make Blast Database Menu

How to create a custom NCBI Blast Database from a FASTA File

Update: Since Blast2GO v.4 or in OmicsBox you can create your Blast Database directly from within the application. See screenshots below. Note: This tutorial is based on the NCBI blast binaries released in 2014 and some parameters might have changed since then If you want to blast your sequences against an own own database you need to create a custom

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