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Metagenomic analysis of two soda lakes, with and without cyanobacterial bloom, with OmicsBox

In this use case we will use the metagenomics tools included in OmicsBox to analyze the microbial communities of two different soda lakes from Brazil. The original study was carried out by Ana P. D. Andreote, et al., 2018 (doi: 10.3389/fmicb.2018.00244). Introduction Soda lakes are special ecosystems found across Africa, Europe, Asia, etc. These lakes show high levels of sodium

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Metagenomic analysis of two soda lakes, with and without cyanobacterial bloom, with OmicsBox

In this use case we will use the metagenomics tools included in OmicsBox to analyze the microbial communities of two different soda lakes from Brazil. The original study was carried out by Ana P. D. Andreote, et al., 2018 (doi: 10.3389/fmicb.2018.00244). Introduction Soda lakes are special ecosystems found across Africa, Europe, Asia, etc. These lakes show high levels of sodium

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Evaluation of Eukaryotic Gene Finding with Augustus in OmicsBox

Evaluation of Eukaryotic Gene Finding with Augustus in OmicsBox

  The OmicsBox Genome Analysis Module 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. We will

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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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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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