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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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CloudBlast and CloudIPS finished, but there are still white sequences.

CloudBlast and CloudIPS need Cloud Units to work.If all Cloud Units have been consumed CloudBlast and CloudIPS will stop. Consumption depends on what you are doing. The most costly (in terms of computation time) analysis is definitely to do a blastx against the whole NR with very long sequences. The smaller the database used the less Cloud Units are used. Use the taxonomy

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new version 5

Release Version 5

Release Date: 13/01/2018) Just in time for the PAG Plant & Animal Genome Conference, we launched Blast2GO 5! This major release brings many new features. Most importantly, Blast2GO is now connected to the powerful BioBam Cloud, an AWS  architecture which gives a big boost to many analysis steps. Details below.  To upgrade from version 4 to 5 you have to

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Coding Potential Assessment Tool

This video shows how to use the ‘Coding-Potential Assessment Tool‘ which allows distinguishing the coding transcripts from the non-coding transcripts. This can be achieved using prebuilt models or building a species-specific model from the NCBI database. The results of the coding potential can be cross-checked with the Blast results and may allow discovering some novel mRNA.

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Changes in Maize Transcriptome due to Virus Infection

BioBam Supported Project: Changes in maize transcriptome in response to Maize Iranian Mosaic Virus (MIMV) infection. Researchers: Mr. Abozar Ghorbani, Ph.D. candidate at Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran Supervisors: Prof. Keramatollah Izadpanah, Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran and A/Prof. Ralf Dietzgen, Queensland Alliance for Agriculture and Food Innovation, the

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