Video Tutorials

Helpful Features, Tips and Tricks

How to translate longest ORFs

The Blast2GO “Translate Longest ORF” tool searches for the longest Open Reading Frame (ORF) in nucleotide sequences and translates them into their protein sequences. You may choose one or multiple of the six possible DNA frames or select the reading frame based on the frame of the best blastx hit. In this video, we will explain how to translate a set of

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How to perform a Gene Set Enrichment Analysis (GSEA)

What is an enrichment analysis? An enrichment analysis is a bioinformatics method which identifies enriched or over-represented gene sets among a list of ranked genes. Gene sets are groups of genes that are functionally related according to current knowledge. Commonly used sets of genes are those sharing biological functions like gene ontology terms, pathways or a common relation like a

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How to use PSORTb

This tutorial shows how to assign subcellular localizations with PSORTb in Blast2GO. We also explain how to merge the obtained results to the existing functional annotations of a Blast2GO project. Blast2GO allows to assigns subcellular localization sites to proteins based on their amino acid sequence via PSORTb. PSORTb is an algorithm which can be applied to bacteria or archaea protein sequences and uses a  probabilistic system

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Coloured Graphs: How to combine multiple functional GO profiles

The Coloured Graph option is a function in Blast2GO which allows to combine and visualize multiple functional profiles within one GO graph. For each group or profile a different color can be assigned and the resulting GO graph can be filtered and colored accordingly. This video shows how to create a text files to generate a Coloured Graph for three

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How to select sequences by function and create ID lists

This tutorial shows how to use the Generic Table and the “Select” functions in Blast2GO to identify sequences based on its biological functions and how to create and combine ID lists. These lists can be saved and used in downstream analysis like e.g. enrichment analysis. In Blast2GO, sequences are shown in table format. Per default, annotation projects use the Blast2GO

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How to perform a Fisher’s Exact Test

Blast2GO allows performing enrichment analysis with a Fisher’s Exact Test. It is a statistical test based on contingency tables to study the significance of the association between two kind of classifications. Blast2GO allows to apply this test to Gene Ontology functional annotations and to compare different gene lists against each other. This is used to identify statistically significant and enrichment

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How to use BioMart and GO-Slim

This short video shows how to use BioMart and GO-Slim to download and review the whole human genome functional annotation with Blast2GO. BioMart allows you to download the functional annotations of many different organisms directly into Blast2GO. BioMart offers many different identifiers like e.g. UniProt, Ensembl, HGNC, etc. Additionally to the annotations, it is also possible to obtain the protein

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How to use RFAM

Blast2GO allows searching for non-coding RNA (ncRNA) families and other structured RNA elements sequences via the RFAM webservice. The RFAM database is a collection of RNA families, categorized into three functional classes: non-coding RNA genes structured cis-regulatory elements self-splicing RNAs The RFAM algorithm allows via alignments to search this database and classify your sequence dataset. This might be interesting for contigs obtained via

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