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A basic evaluation of the Coding-Potential Assessment Tool

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

White sequences in CloudBlast and CloudIPS

Mariana Monteiro March 16, 2017

CloudBlast and CloudIPS need Cloud Units to work.If all Cloud Units have been consumed CloudBlast and CloudIPS will stop. Consumption depends on what you are doing. The most costly (in terms of computation time) analysis is definitely to do a blastx against the whole NR with very long sequences. The smaller the database used the less Cloud Units are used. Use the taxonomy

Release Version 5

Stefan Götz March 16, 2017

Release Date: 13/01/2018) Just in time for the PAG Plant & Animal Genome Conference, we launched Blast2GO 5! This major release brings many new features. Most importantly, Blast2GO is now connected to the powerful BioBam Cloud, an AWS architecture which gives a big boost to many analysis steps. Details below. To upgrade from version 4 to 5 you have to

Coding Potential Assessment Tool

Mariana Monteiro March 15, 2017

This video shows how to use the ‘Coding-Potential Assessment Tool’ which allows distinguishing the coding transcripts from the non-coding transcripts. This can be achieved using prebuilt models or building a species-specific model from the NCBI database. The results of the coding potential can be cross-checked with the Blast results and may allow discovering some novel mRNA.

Changes in Maize Transcriptome due to Virus Infection

Mariana Monteiro March 5, 2017

BioBam Supported Project: Changes in maize transcriptome in response to Maize Iranian Mosaic Virus (MIMV) infection. Researchers: Mr. Abozar Ghorbani, Ph.D. candidate at Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran Supervisors: Prof. Keramatollah Izadpanah, Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran and A/Prof. Ralf Dietzgen, Queensland Alliance for Agriculture and Food Innovation, the

Run blast icon greyed out in OmicsBox

Mariana Monteiro February 25, 2017

After loading the sequences, the run blast icon is greyed out in OmicsBox, why? It is possible to load more than one project into OmicsBox and each project will be displayed in a different tab.So to run the analysis on the different projects you will need to have the OmicsBox table active (white tab). In your case, probably the Progress

Enrichment analysis on 2 groups of sequences

Mariana Monteiro January 31, 2017

It is possible to perform a Fisher Exact Test on the 2 groups even if the annotation is in different files (.annot). First, both .annot files (group 1 and group 2) need to be loaded into Blast2GO.The test and reference set have to be generated according to the groups you want to compare. These are normal text files with the

NCBI GenBank Submission

Carlos Menor November 16, 2016

This video shows how to use the ‘Create NCBI GenBank Genome Submission Files’ tool which allows to generate all files (e.g. the Asn1 (.sqn) file) necessary to submit your annotated sequences to the NCBI database. It allows to combine genomic sequences and functional annotations and creates valid GenBank submission files. Additionally, this video explains how to obtain source files (.gff and .annot files), provides

Time-Course Differential Expression Analysis

Carlos Menor November 15, 2016

The Time Course Expression Analysis tool allows performing a differential expression analysis of expression data arising from a time course RNA-seq experiment. This application is based on the maSigPro Bioconductor package, which implements a two-step regression strategy to detect genes with significant temporal expression changes and significant differences between experimental groups. This video shows the analysis of count data coming

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A basic evaluation of the Coding-Potential Assessment Tool

White sequences in CloudBlast and CloudIPS

Release Version 5

Coding Potential Assessment Tool

Changes in Maize Transcriptome due to Virus Infection

Run blast icon greyed out in OmicsBox

Enrichment analysis on 2 groups of sequences

NCBI GenBank Submission

Time-Course Differential Expression Analysis

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