Use Cases, Reviews, Tutorials Archives

Metagenomic analysis of microbial communities with OmicsBox

Jesus Gutierrez October 22, 2019

In this use case we will use the metagenomics tools included in OmicsBox to analyze the microbial communities of two different soda lakes from Brazil. The original study was carried out by Ana P. D. Andreote, et al., 2018 (doi: 10.3389/fmicb.2018.00244). Introduction Soda lakes are special ecosystems found across Africa, Europe, Asia, etc. These lakes show high levels of sodium

Transcriptome analysis of Acinetobacter baumannii cells under different conditions

Mariana Monteiro June 11, 2019

OmicsBox Supported Project Researchers: Background and Project Overview: A.baumannii, a nosocomial pathogen, ranks first in the WHO’s list of antibiotic-resistant priority pathogen. The problem of increasing frequency of multi-drug resistance in A. baumannii has been further compounded by tolerance to high concentration of antibiotics due to persister cells. Persister cells are phenotypic variants of normal cells that are formed in

Lipid transcriptome profiling of indigenous Dunaliella sp. isolate

Mariana Monteiro March 20, 2019

BioBam Bioinformatics S.L. Supported Project. Researchers: Nahid Hosseinzadeh Gharajeh Mohammad Amin Hejazi Mostafa Valizadeh Ebrahim Dorani Background and Project Overview: Dunaliella is a unicellular, halotolerant, biflagellate microalga which is already exploited as a platform in food, feed, aquaculture, biomedical, pharmaceutical, nutraceutical and cosmeceutical industries, specifically due to its high production of β-carotene and fine chemicals. There is a wide range

Whole Genome Functional Annotation of Solanum lycopersicum

David Seide March 6, 2019

Whole genome functional annotation of Solanum lycopersicum with OmicsBox functional annotation module.

Expression quantification and differential expression analysis

Carlos Menor November 20, 2018

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

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, 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

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Metagenomic analysis of microbial communities with OmicsBox

Transcriptome analysis of Acinetobacter baumannii cells under different conditions

Lipid transcriptome profiling of indigenous Dunaliella sp. isolate

Whole Genome Functional Annotation of Solanum lycopersicum

Expression quantification and differential expression analysis

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

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End-to-End Analysis of Long Reads in OmicsBox

Cutting-Edge Long-Read Transcriptomics Research Published in Nature Methods

Single Cell RNA-Seq analysis of Arabidopsis thaliana roots

Population Structure Analysis with OmicsBox

IsoQuant: Long-Read Isoform Identification and Quantification

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