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Time-Course Differential Expression Analysis

The Time Course Expression Analysis tool allows performing a differential expression analysis of expression data arising from a time course RNA-seq experiment. This application is based on the maSigPro Bioconductor package, which implements a two-step regression strategy to detect genes with significant temporal expression changes and significant differences between experimental groups. This video shows the analysis of count data coming

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A basic evaluation of eukaryotic gene finding with Augustus in Blast2GO

Blast2GO allows executing eukaryotic de-novo and RNA-seq based gene finding with Augustus. In this way, it is possible to discover novel, putative coding genes and their genomic positions for yet uncharacterized genome. Based on the Augustus algorithm an ‘ab-initio’ (DNA sequences only), as well as RNA-seq guided (BAM files) gene predictions, are supported. As shown below, the latter increases prediction

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Pairwise Differential Expression Analysis

The Pairwise Differential Expression Analysis tool is designed to perform differential expression analysis of count data arising from an RNA-seq experiment. The application, which is based on the software package “edgeR”, allows the identification of differentially expressed genes between two experimental conditions by applying quantitative statistical methods. This video shows the performance of a pairwise differential expression analysis in which

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Time Course Expression Analysis

A simple use-case comparing Blast2GO with R chunks The Blast2GO feature “Time Course Expression Analysis” is designed to perform time-course expression analysis of count data arising from RNA-seq technology. Based on the software package ‘maSigPro’, which belongs to the Bioconductor project, this tool allows the detection of genomic features with significant temporal expression changes and significant differences between experimental groups

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Pairwise Differential Expression Analysis

A simple use-case comparing Blast2GO with R chunks The Blast2GO feature “Pairwise Differential Expression Analysis” is designed to perform differential expression analysis of count data arising from RNA-seq technology. This tool allows the identification of differential expressed genes considering two different conditions based on the software package ‘edgeR’, which belongs to the Bioconductor project. This use case shows the basic

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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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New Blast2GO Version 3.3

Major Release Version 4

(Release Date: 13/09/2016) We are very happy to announce the release of Blast2GO 4. This new version contains many new bioinformatic features like Differential Expression Analysis, Gene Finding or Gene Set Enrichment Analysis. 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

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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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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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