blast2go Archives

Generate Gene Venn Diagram Representations with OmicsBox

Miguel Ferrando November 6, 2023

What is a Gene Venn Diagram? A Gene Venn Diagram is a graphical representation in the form of overlapping circles widely used to represent relationships among different genes (IDs). High-throughput sequencing technologies generate large amounts of data sets coming from multiomics studies. At the transcriptomic level, differential expression analysis appears to be a highly important field of study in bioinformatics

InterProScan with Blast2GO: How to make it work again

David Seide March 8, 2021

Activate development on Blast2GO was discontinued in 2018. All its functionality and more new features are now part of OmicsBox. Because Blast2GO is no longer updated, some of its functions may have stopped working because web services have changed or security certificates have expired, among other things. It is highly recommended to use OmicsBox instead of Blast2GO to benefit from

De novo genome assembly and annotation of fungus in OmicsBox

Marta Benegas Coll March 13, 2020

This project reproduces the study carried out by Hittalmani S. et al. in 2016 about the S. oryzae fungus, which causes sheath rot of rice. We used OmicsBox for all necessary steps till functional analysis in order to predict pathogenic functions. (Original research paper: https://doi.org/10.1186/s12864-016-2599-0)

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,

Whole Genome Functional Annotation of Solanum lycopersicum

David Seide March 6, 2019

Whole genome functional annotation of Solanum lycopersicum with OmicsBox functional annotation module.

How to export Gene Finder GFF output with GO terms.

Mariana Monteiro November 22, 2018

This article explains how to export a GFF file with GO terms in Blast2GO.

Enrichment Analysis from pairwise differential expression results in OmicsBox

Mariana Monteiro November 13, 2018

This article explains how to start functional enrichment analysis of pairwise differential genes in Blast2GO.

How to create a gene list within OmicsBox to run the functional enrichment analysis

Mariana Monteiro November 13, 2018

This article explains how to create ID lists of either Blast results or differential expressed genes in Blast2GO.

How to change sequence names coming from Prokaryotic GeneFinding

Mariana Monteiro November 12, 2018

When running GeneFinding the sequences receive a name with the predicted genes. The first part of the sequence identifier comes from the genome reference sequence name (de-novo assembly) and then a _orfx is appended, where x is a number. Sometimes this name is not useful to proceed with downstream analysis or compare results from other experiments. Is there any way

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Generate Gene Venn Diagram Representations with OmicsBox

InterProScan with Blast2GO: How to make it work again

De novo genome assembly and annotation of fungus in OmicsBox

Transcriptomic response of A. galli to an anthelmintic drug

Whole Genome Functional Annotation of Solanum lycopersicum

How to export Gene Finder GFF output with GO terms.

Enrichment Analysis from pairwise differential expression results in OmicsBox

How to create a gene list within OmicsBox to run the functional enrichment analysis

How to change sequence names coming from Prokaryotic GeneFinding

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