OmicsBox Archives - Page 3 of 5

Identification and Expression analysis of genes involved in endodormancy break in potato.

Mariana Monteiro March 31, 2020

BioBam Scholarship Supported Project – with OmicsBox. Researchers: Madhuri Gupta Dr. Pushpender Kumar Project and Overview At harvest, potato (Solanum tuberosum L.) tubers, one of the most important crops among vegetables, are dormant and will not sprout. Tubers contain shoot apical meristems on their surface with the ability to differenciate and grow into a new clone of the parent plant.

Comparing taxonomic and functional compositions in metagenomic samples

Jesus Gutierrez March 17, 2020

Any annotation of metagenomic sequences, whether it involves pathways, clusters of orthologous genes, species or any other taxonomic or functional classification can be compared across samples. These analyses are encompassed within the Differential Abundance Analysis, and they require robust statistical approaches to achieve reliable results because metagenomics datasets often show under-sampling and low signal-to-noise ratios. All differential abundance analyses can

Draft genome of a new Verminephrobacter eiseniae strain

Mariana Monteiro March 10, 2020

BioBam Scholarship Supported Project – with OmicsBox. Researchers: Mr. Arun Arumugaperumal Mr. Sayan Paul and Miss Saranya Lathakumari, PhD students Dr. Sudhakar Sivasubramaniam Abstract The earthworm Eisenia fetida has a symbiotic bacteria named Verminephrobacter eiseniae in its nephridia. A new strain of V. eiseniae msu was found out and the genome of the bacteria was found hidden in the genome

Exploring transcriptome completeness in OmicsBox with BUSCO

Carlos Menor February 4, 2020

De novo transcriptome assemblies are required to analyze RNA-seq data from a species for which there is no reference genome. Once the assembly is complete, researchers need to know how good it is or compare the quality of similar assemblies generated by different parameters. There are several ways to characterize the quality of transcriptome assemblies. A good metric of assembly

Hybrid Genome Assembly in OmicsBox with SPAdes

Carlos Menor February 4, 2020

DNA sequencing is the process of determining the nucleic acid sequence in DNA, and it is the technology by which the genome of a species can be characterized. Despite the advent of next-generation sequencing, current DNA sequencing technologies cannot read whole genomes at once, but rather reads small pieces of between 20 and 30.000 bases, depending on the technology used.

How to run Blast of the differential expressed genes?

Mariana Monteiro December 10, 2019

It is possible to run Blast only on the differential expressed genes and not on all the data with OmicsBox. One has to select only those sequences that have differential expressed genes in the OmicsBox project.First, make sure that the name of the sequences in the project match the ones from the differential expression results.

Multilocus Sequence Typing MLST Analysis Tool

Carlos Menor July 29, 2019

The Multilocus Sequence Typing Analysis Tool of OmicsBox (MLST) is a nucleotide sequence-based approach of characterizing isolates of bacterial species using the sequences of internal fragments of seven housekeeping genes. This video shows step-by-step how to analyze bacterial sequences with the MLST App in OmicsBox. As input, users can provide either DNA-Seq reads in FASTQ or contigs/scaffolds in FASTA format.

How to create a taxonomic mapping file.

Mariana Monteiro July 29, 2019

Create a taxonomic mapping file to Make Blast Database within OmicsBox OmicsBox allows creating a custom database to run Blast locally. The blast algorithm will run on the user’s computer against a database that is installed locally.In order to do so, we have to either download a pre-formatted NCBI database (see tutorial) or format our own database (see this tutorial

OmicsBox Video Introduction

Stefan Götz July 9, 2019

This 5-minute video provides a brief introduction to OmicsBox. All main features of all modules are introduced. OmicsBox is a bioinformatics Solution to easy your Omcis Data Analysis. Our workflows get you from raw reads tp insights fast and easy. The presented modules include Transcriptomics, Functional Annotation and Analysis with Blast2GO, the Genome Analysis Module as well as the Metagenomics

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Identification and Expression analysis of genes involved in endodormancy break in potato.

Comparing taxonomic and functional compositions in metagenomic samples

Draft genome of a new Verminephrobacter eiseniae strain

Exploring transcriptome completeness in OmicsBox with BUSCO

Hybrid Genome Assembly in OmicsBox with SPAdes

How to run Blast of the differential expressed genes?

Multilocus Sequence Typing MLST Analysis Tool

How to create a taxonomic mapping file.

OmicsBox Video Introduction

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