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Sarocladium oryzae

De novo genome assembly and annotation of sheath rot fungus Sarocladium oryzae with Blast2GO

This project reproduces a study carried out by Hittalmani S. et al. in 2016 about the S. oryzae fungus which causes sheath rot of rice. We used Blast2GO for the main analysis steps like the structural and functional annotation and analysis. (Original research paper: https://doi.org/10.1186/s12864-016-2599-0) 1.  Introduction Sheath rot disease caused by S. oryzae is an emerging threat to rice

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A. galli

Reanalyzing the A. galli transcriptomic response to an anthelmintic drug with Blast2GO

In this analysis, we will reproduce the study that was carried out by Michaela M. Martis et al. in 2017 (doi: http://doi.org/10.1371/journal.pone.0185182) with Blast2GO. Introduction Ascaridia galli is an intestinal parasite which infects a wide range of domestic birds. It is especially important in European farms, where it parasites laying hens and cause some economic problems. The only available treatments are

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How to create analysis workflows

OmicsBox/Blast2GO provides an interface to create, edit and run workflows based on the Common Workflow Language (CWL) specification. This interface allows to describe all analysis steps using the functions and tools offered by Blast2GO and connect them to perform a complete analysis in a single run.  This video shows step-by-step how to create a workflow from scratch, define the input

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Expression Estimation at Transcript-Level

The Transcript-level Quantification feature of OmicsBox/Blast2GO allows quantifying the gene and isoform expression of RNA-seq datasets. This video shows step-by-step how to create a count table of aligned sequencing reads and explains in detail the different concepts of expression quantification at transcript level. The application is based on the RSEM software package, which assigns reads to the isoforms they came

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Debabrata

Is Repeat-Masking necessary in Blast2GO?

Does RNA-seq-based Eukaryotic GeneFinding of Blast2GO require repeat-masking the whole genome shotgun (WGS) sequence? A case study in jute (Corchorus olitorius L., Malvaceae s. l.) Debabrata Sarkar1, Carlos Menor2 and Nagendra Kumar Singh3 1Biotechnology Unit, Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres (CRIJAF), Nilganj, Barrackpore, Kolkata 700120, West Bengal, India. E-mail: debabrata.sarkar@icar.gov.in. ORCID iD: 0000-0003-3943-96462Blast2GO Team,

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Pneumocystis

Evolutionary analysis of three Pneumocystis genomes

Blast2GO Supported Project. Researchers: Prof. Luis Delaye, CINVESTAV Irapuato, México Prof. Enrique Calderon, Instituto de Biomedicina de Sevilla, España Prof. Andrés Moya, I2SysBio, Universidad de Valencia, España Background and Project Overview: Fungi from the genus Pneumocystis parasites lungs of mammals. These fungi show extensive stenoxenism, meaning that each Pneumocystis specie parasites a single mammal species. In humans, Pneumocystis causes pneumonia

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Study of gene expression patterns associated with reproductive plasticity in the peacock blenny Salaria pavo

Blast2GO Supported Project. Researchers: MSc Sara D. Cardoso, Ph.D. candidate at Gulbenkian Institute for Science (IGC), Oeiras, Portugal Supervisors: Prof. Rui F. Oliveira, Gulbenkian Institute for Science (IGC), Oeiras, Portugal and Prof. Adelino V. M. Canário, CCMAR – Centre of Marine Sciences, University of Algarve, Faro, Portugal Background and Project Overview: The peacock blenny Salaria pavo (family Blenniidae) is a

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Expression Quantification at Gene-Level

The “Create Count Table” feature of OmicsBox/Blast2GO allows quantifying the gene expression of RNA-seq datasets. This video shows step-by-step how to create a count table of raw reads and explains in detail different concepts of expression quantification. The available parameters are inspired by the popular HTSeq Python Package (reference below).

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A basic evaluation of the Coding-Potential Assessment Tool in Blast2GO

RNA-seq technologies detect coding as well as multiple forms of noncoding RNA. RNA-seq can accurately measure gene and transcript abundance as well as identify known and novel features of a transcriptome. While the coding transcripts will lead to effector proteins, the non-coding transcripts are usually involved in the gene expression regulation and in the transcription and translation machinery. In this

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