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Tutorial: some parts of the application are not working.

Alejandro Rocamonde June 8, 2016

(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

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How to run Blast2GO installer in Linux systems?

Alejandro Rocamonde June 2, 2016

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?

Alejandro Rocamonde May 31, 2016

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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New Blast2GO Version 3.3

New Version 3.3

Stefan Götz May 19, 2016

(Release Date: 9/05/2016) We are very happy to announce the latest release of Blast2GO 3.3. Blast2GO will update automatically if activated. Otherwise please download the latest version online from here. Feedback, questions, as well as feature requests, are most welcome. Please write to us: support@biobam.com

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new version3.2 final

New Version 3.2

Stefan Götz January 28, 2016

(Release Date: 29/01/2016) We are very happy to announce the release of a new version of Blast2GO. Version 3.2 comes with many new features and improvements. Blast2GO will update automatically if activated. Otherwise please download the latest version online from here. We hope you will take advantage of these improvements. Feedback, questions, as well as feature requests, are most welcome. Please

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

Robert Nica January 24, 2016

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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Brief review: Gene-Finding for Bacterial Genomes

Mariana Monteiro November 24, 2015

Introduction You have: Newly aligned genome of a bacterial non-model organism. You want: Perform functional annotation and analysis of its potential proteins. You need: Predict all potential genes or coding regions before proceeding to the functional annotation: Gene-Finding How can this be done? Use Glimmer, a set of algorithms which uses interpolated Markov models to distinguish coding from non-coding DNA in bacteria, archaea, and viruses. Glimmer

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Reformat Uniprot/Swissprot Species Distribution

Mariana Monteiro November 23, 2015

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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Blast2GO PRO Plugin for CLC bio Genomics Workbench Update

David Seide November 3, 2015

(Release Date: 3 November 2015) We released a new version (v.1.4.4) of our successful Blast2GO PRO Plugin for the CLC bio Genomics Workbench with new features and improvements. New features: Batch Rename your sequence names Set To Sense: Switch the sense of your sequences based on the best blast hit frame Longest ORF: Crop and convert sequences to longest ORF

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