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Expression quantification and differential expression analysis

Expression quantification and differential expression analysis

One of the most common applications of RNA-seq is to estimate gene and transcript expression. It starts with the alignment or mapping of reads and there are two possible alternatives: mapping to the genome when a reference sequence is available or mapping to the transcriptome (e.g. de novo assembled transcriptome). Reads may map uniquely or could be multi-mapped reads, while

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de-novo transcriptome overview

Learn about de-novo transcriptome assembly

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

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previous diagram

Basic Transcriptome Characterization with Blast2GO

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

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quality check

NGS Preprocessing and Quality Control: How-To with OmicsBox

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

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

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

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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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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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