Jesus Gutierrez

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

Jesus Gutierrez March 23, 2020

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

Comparing taxonomic and functional compositions in metagenomic samples

Jesus Gutierrez March 17, 2020

Any annotation of metagenomic sequences, whether it involves pathways, clusters of orthologous genes, species or any other taxonomic or functional classification can be compared across samples. These analyses are encompassed within the Differential Abundance Analysis, and they require robust statistical approaches to achieve reliable results because metagenomics datasets often show under-sampling and low signal-to-noise ratios. All differential abundance analyses can

Transcriptomic response of A. galli to an anthelmintic drug

Jesus Gutierrez October 24, 2019

In this analysis, we will reproduce a study carried out by Michaela M. Martis et al. in 2017 with OmicsBox. (http://doi.org/10.1371/journal.pone.0185182) Introduction Ascaridia galli is an intestinal parasite that infects a wide range of domestic birds. It is especially important in European farms, where it parasites laying hens and causes economic problems. The only available treatments are the Benzimidazole derivatives,

Metagenomic analysis of microbial communities with OmicsBox

Jesus Gutierrez October 22, 2019

Combine differential expression results with functional annotation in OmicsBox

Jesus Gutierrez April 18, 2019

Once differential expression results are retrieved, it could be interesting to assign functional annotations to the differentially expressed genes and visualize the results in a single project. This is possible in OmicsBox.

Basic Transcriptome Characterization with Blast2GO

Jesus Gutierrez November 13, 2018

Analysis workflow Objective: To describe the process of a transcriptome characterization using Blast2GO. Input data: A mouse RNA-seq dataset composed of 140803 contigs. Pipeline: Blastx and InterproScan were performed with the complete dataset to identify proteins. Sequences with no Blastx hits nor IPS results were selected and further analyzed. RFAM and Local Blast (against an EST mouse db) were performed with the sequences with

Improve functional annotations using “Retrieve Blast Top-hit”

Jesus Gutierrez November 13, 2018

RNA-seq data is sometimes difficult to match with proteins, due to the short length of the reads. When this is the case, it might be useful to try to find EST hits, which can then be used to find new protein matches. In this demo, we will show how to retrieve top EST hits and the different options that this tool

New RNA-Seq Features in Blast2GO 5

Jesus Gutierrez October 31, 2018

This video shows an overview of new RNA-Seq features in Blast2GO 5: FastQ Quality Control and Preprocessing, de novo Transcriptome Assembly, Transcript Quantification and Differential Expression Analysis.

How to translate longest ORFs

Jesus Gutierrez September 14, 2016

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

Comparing taxonomic and functional compositions in metagenomic samples

Transcriptomic response of A. galli to an anthelmintic drug

Metagenomic analysis of microbial communities with OmicsBox

Combine differential expression results with functional annotation in OmicsBox

Basic Transcriptome Characterization with Blast2GO

Improve functional annotations using “Retrieve Blast Top-hit”

New RNA-Seq Features in Blast2GO 5

How to translate longest ORFs

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