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Metatranscriptomics Analysis of Macaques with Idiopathic Chronic Diarrhea (ICD)

1. Introduction Juvenile rhesus macaques commonly suffer from idiopathic chronic diarrhea (ICD). This disease is characterized by inflammation of the colon and repeated bouts of diarrhea. It is a common cause of morbidity and mortality among macaques because it is unresponsive to drugs. The gut microbiome of macaques with ICD is characterized by abrupt changes when compared to healthy individuals.

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courtship song Laupala crickets

Zeroing in on genes involved in courtship song variation in Laupala crickets

OmicsBox Supported Project. Researchers: Hayden Waller, Cornell University, USA Background and Project Overview: One of the primary outcomes of speciation – the formation of new species – is the generation of pre-mating barriers that prevent or greatly reduce gene flow. Behavioral changes are perhaps the most potent in the early stages of speciation. In particular, the divergent evolution of sexual

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Clustering redundant transcripts in OmicsBox with CD-HIT

De novo transcriptome assemblies are required to analyze RNA-seq data from a species for which there is no reference genome. However, with the advancement of next-generation sequencing technologies, the amount of available sequencing data is growing exponentially. Because of this, assembly algorithms often generate a large number of transcripts. Removing redundancy from such data could be crucial for reducing storage space,

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Datura Metal

De novo transcriptome analysis in Datura metel and identification of genes related to withanolides biosynthesis pathway

BioBam Scholarship Supported Project – with OmicsBox. Researchers: Madhavi Hewadikaram Dr Sanjaya Deepal Bathige Prof. Veranja Karunaratne Project overview Withanolides are secondary plant compounds that belong to a family of C28 ergostane-type steroidal δ lactones that mainly belong to the family Solanaceae of the plant kingdom. Withanolides have held the interest and its importance in the scientific community owing to

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Solanum tuberosum

Identification and Expression analysis of genes involved in endodormancy break in potato (Solanum tuberosum L.)

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.

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Busco OmicsBox Screenshot

Exploring transcriptome completeness in OmicsBox with BUSCO

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

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Predict coding regions within transcripts in OmicsBox with TransDecoder

Most transcripts assembled from eukaryotic and prokaryotic RNA-Seq data are expected to code for proteins. The most practical procedure to identify likely coding transcripts is a sequence homology search, such as by BLASTX, against sequences from a well-annotated and related species. Predicting coding regions is crucial to determine the molecular role that transcripts play in the cell. Unfortunately, such well-annotated

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How to run Blast of the differential expressed genes?

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.

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Busco OmicsBox Screenshot

New Transcriptomics Features

Release OmicsBox version 1.2 (24th of October, 2019) We are happy to announce the following updates for the transcriptomics module. New features include Completeness Assessment and Predict Coding Regions. More details can be found below as well as in the online user manual and Transcriptomics Module website. Completeness Assessment The Completeness Assessment functionality provides quantitative measures for the assessment of transcriptome assembly completeness, based on

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