fbpx

Blog

News, Tutorials, Tips and Tricks

Brief review: Gene-Finding for Bacterial Genomes

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

Read More »

Amazon AWS NCBI Blast Search

(This feature is now obsolete.) In the following article, I will explain how to set up an EC2 instance with the Blast+ AMI. This NCBI webpage takes us to the most recent Blast+ AMI in the AWS Marketplace, which we want to configure after hitting “Continue” on the right-hand side. We can now play around with the Region and EC2

Read More »

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

Read More »

Blast2GO PRO Plugin for CLC bio Genomics Workbench Update

(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

Read More »
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

Read More »

Blast2GO Command Line Features 1.1.4

(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.

Read More »

Command Line Examples

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.

Read More »

Blast2GO Release Version 3.1

(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.

Read More »

Blog Categories:

News

Releases, Media, Announcements, etc.

Tips And Tricks

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

Video Tutorials

Helpful Features, Tips and Tricks

Use Cases, Reviews, Tutorials

Product Tutorial, Quickstarts, New Features, etc.

Most Popular: