Use Cases, Reviews, Tutorials

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Functional Analysis of Pancreatic Cancer Expression Profiles

This use case shows how to perform a functional analysis of pancreatic cancer expression data with Blast2GO. The performed steps are explained more in detail with short video tutorial linked to each section. Malignant (PDAC), benign (CP) and normal tissue (NP) gene lists are compared against each other. The human genome functional annotation data is retrieved via BioMart and used

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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

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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

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Command Line Examples

New 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.

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