Use Cases, Reviews, Tutorials Archives - Page 5 of 6

Learn about de-novo transcriptome assembly

Carlos Menor November 20, 2018

High-throughput sequencing of RNA has revolutionized the study of species for which a reference genome is not available or incomplete by enabling the large-scale analysis of their transcriptomes. While analyses of model organisms generally rely on a reference genome, studies of non-model organisms usually lack this advantage. In the absence of an appropriate reference genome, de novo transcriptome assembly is

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

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, offers 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

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

Carlos Menor August 2, 2018

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

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

Study of gene expression patterns associated with reproductive plasticity in the 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

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

Carlos Menor March 27, 2017

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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Learn about de-novo transcriptome assembly

Basic Transcriptome Characterization with Blast2GO

NGS Preprocessing and Quality Control: How-To with OmicsBox

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

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

Is Repeat-Masking necessary in Blast2GO?

Evolutionary analysis of three Pneumocystis genomes

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

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

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Bioinformatic analysis of some gene expressions involved in berries growth

Mining Genes involved in Biodegradation of Tannery Wastes through Metagenomics Analysis of Microbial Communities in a Hyperalkaline Spring at Manleluag, Pangasinan

We are proud to announce that we have received a grant from the Valencian Innovation Agency – AVI

rRNA Removal with SortMeRNA in OmicsBox

Metagenomics Contaminant Removal with Bowtie

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