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