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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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Select .pal files to Run LocalBlast

Run Local Blast within OmicsBox

Mariana Monteiro October 16, 2015

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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Blast2GO Command Line Features 1.1.4

David Seide September 25, 2015

(Release Date: 01/10/2015) You can now perform Blast and InterProScan from within the CLI, which means you can run the whole functional annotation analysis with just one command. Find here some useful command line examples.

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Command Line Examples

Stefan Götz September 25, 2015

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. Request your trail here.

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Blast2GO Release Version 3.1

Stefan Götz August 1, 2015

(Release Date: 01/08/2015) This new version allows to work with multiple projects in parallel, a new FileManger to organizer all your data, run RFAM analysis and much more.

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Make Blast Database Menu

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

Mariana Monteiro November 28, 2014

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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