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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

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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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Debabrata

Is Repeat-Masking necessary in Blast2GO?

Mariana Monteiro July 24, 2017

Does RNA-seq-based Eukaryotic GeneFinding of Blast2GO require repeat-masking the whole genome shotgun (WGS) sequence? A case study in jute (Corchorus olitorius L., Malvaceae s. l.) Debabrata Sarkar1, Carlos Menor2 and Nagendra Kumar Singh3 1Biotechnology Unit, Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres (CRIJAF), Nilganj, Barrackpore, Kolkata 700120, West Bengal, India. E-mail: debabrata.sarkar@icar.gov.in. ORCID iD: 0000-0003-3943-96462Blast2GO Team,

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Pneumocystis

Evolutionary analysis of three Pneumocystis genomes

Mariana Monteiro July 17, 2017

Blast2GO Supported Project. Researchers: Prof. Luis Delaye, CINVESTAV Irapuato, México Prof. Enrique Calderon, Instituto de Biomedicina de Sevilla, España Prof. Andrés Moya, I2SysBio, Universidad de Valencia, España Background and Project Overview: Fungi from the genus Pneumocystis parasites lungs of mammals. These fungi show extensive stenoxenism, meaning that each Pneumocystis specie parasites a single mammal species. In humans, Pneumocystis causes pneumonia

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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

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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

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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

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Evaluation of Eukaryotic Gene Finding with Augustus in OmicsBox

Evaluation of Eukaryotic Gene Finding with Augustus in OmicsBox

Carlos Menor October 17, 2016

  The OmicsBox Genome Analysis Module allows executing eukaryotic de-novo and RNA-seq based gene finding with Augustus. In this way, it is possible to discover novel, putative coding genes and their genomic positions for yet uncharacterized genome. Based on the Augustus algorithm an ‘ab-initio’ (DNA sequences only), as well as RNA-seq guided (BAM files) gene predictions, are supported. We will

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Time Course Expression Analysis

Carlos Menor October 6, 2016

A simple use-case comparing OmicsBox with R chunks for Time Course Expression Analysis The Blast2GO feature “Time Course Expression Analysis” is designed to perform time-course expression analysis of count data arising from RNA-seq technology. Based on the software package ‘maSigPro’, which belongs to the Bioconductor project, this tool allows the detection of genomic features with significant temporal expression changes and

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