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NGS Preprocessing and Quality Control: How-To with OmicsBox

Carlos Menor September 5, 2018

Functional genomics attempts to describe the functions of genes and proteins by making use of data derived from genomic and transcriptomic experiments. Some bioinformatics tools, like OmicsBox, offer biologists to get from raw NGS data through all steps up to the generation of biological insights for a species without any previous genome resources. The bioinformatic process to perform a de

Gene expression profiling in fresh-water colonial green alga Volvox carteri

Mariana Monteiro August 21, 2018

Blast2GO Supported Project. Researchers: Mrs.Soulmaz Ekhtari Teachers: Dr. Jafar Razeghi, Dr. Karim Hasanpur, and Dr. Arash Kianianmomeni Background and Project Overview: The evolutionary origin of some multicellular organisms has not yet been completely studied. A clear characteristic of complex multicellular organisms is germ-soma differentiation. The monophyletic group of volvocine contains multiple algae species ranging from unicellular species such as Chlamydomonas reinhardtii

Release Version 5.2

Mariana Monteiro August 8, 2018

(Release Date: 02/08/2018) We are happy to announce that Blast2GO 5.2 has now been released. This update makes our bioinformatics tool for straightforward functional genomics even better.Read below to learn which features and improvements are part of this release. Main features: Venn Diagrams that are fully customizable and allows multiple list comparisons FastQ Pre-Processing (Adapters, Quality, Length) with multiple trimming options.

How to create analysis workflows

Carlos Menor February 8, 2018

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

Expression Estimation at Transcript-Level

Carlos Menor October 20, 2017

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

Is Repeat-Masking necessary in Blast2GO?

Mariana Monteiro July 24, 2017

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,

Evolutionary analysis of three Pneumocystis genomes

Mariana Monteiro July 17, 2017

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

Gene expression study of peacock blenny Salaria pavo

Mariana Monteiro June 2, 2017

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

Expression Quantification at Gene-Level

Carlos Menor April 7, 2017

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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NGS Preprocessing and Quality Control: How-To with OmicsBox

Gene expression profiling in fresh-water colonial green alga Volvox carteri

Release Version 5.2

Expression Estimation at Transcript-Level

Is Repeat-Masking necessary in Blast2GO?

Evolutionary analysis of three Pneumocystis genomes

Gene expression study of peacock blenny Salaria pavo

Expression Quantification at Gene-Level

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