Mariana Monteiro – Page 5

Gene expression study of peacock blenny Salaria pavo

Mariana Monteiro June 2, 2017

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

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

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

How to use PSORTb

Mariana Monteiro August 31, 2016

This tutorial shows how to assign subcellular localizations with PSORTb in OmicsBox/Blast2GO. We also explain how to merge the obtained results to the existing functional annotations of a Blast2GO project. OmicsBox/Blast2GO allows to assigns sub-cellular localization sites to proteins based on their amino acid sequence via PSORTb. PSORTb is an algorithm which can be applied to bacteria or archaea protein sequences

How to select sequences by function and create ID lists

Mariana Monteiro August 9, 2016

This tutorial shows how to use the Generic Table and the “Select” functions in Blast2GO to identify sequences based on its biological functions and how to create and combine ID lists. These lists can be saved and used in downstream analysis like e.g. enrichment analysis. In Blast2GO, sequences are shown in table format. Per default, annotation projects use the Blast2GO

Brief review: Gene-Finding for Bacterial Genomes

Mariana Monteiro November 24, 2015

Introduction You have: Newly aligned genome of a bacterial non-model organism. You want: Perform functional annotation and analysis of its potential proteins. You need: Predict all potential genes or coding regions before proceeding to the functional annotation: Gene-Finding How can this be done? Use Glimmer, a set of algorithms which uses interpolated Markov models to distinguish coding from non-coding DNA in bacteria, archaea, and viruses. Glimmer

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Gene expression study of peacock blenny Salaria pavo

White sequences in CloudBlast and CloudIPS

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

How to use PSORTb

How to select sequences by function and create ID lists

Brief review: Gene-Finding for Bacterial Genomes

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