Machado: open source genomics data integration framework.

Abstract. Background: Genome projects and multiomics experiments generate huge volumes of data that must be stored, mined, and transformed into useful knowledge. All this information is supposed to be accessible and, if possible, browsable afterwards. Computational biologists have been dealing with this scenario for more than a decade and have been implementing software and databases to meet this challenge. The GMOD's (Generic Model Organism Database) biological relational database schema, known as Chado, is one of the few successful open source initiatives; it is widely adopted and many software packages are able to connect to it. Findings: We have been developing an open source software package named Machado, a genomics data integration framework implemented in Python, to enable research groups to both store and visualize genomics data. The framework relies on the Chado database schema and, therefore, should be very intuitive for current developers to adopt it or have it running on top of already existing databases. It has several data-loading tools for genomics and transcriptomics data and also for annotation results from tools such as BLAST, InterproScan, OrthoMCL, and LSTrAP. There is an API to connect to JBrowse, and a web visualization tool is implemented using Django Views and Templates. The Haystack library integrated with the ElasticSearch engine was used to implement a Google-like search, i.e., single auto-complete search box that provides fast results and filters. Conclusion: Machado aims to be a modern object-relational framework that uses the latest Python libraries to produce an effective open source resource for genomics research.Na publicação: Adhemar Zerlotini

Detecção e análise bioinformática de genes sob evidência de seleção positiva em genomas de parasitos.

A relação ecológica de parasitismo é uma constante corrida armamentista entre os organismos parasitas e seus hospedeiros. A infecção por parasitas diminui a aptidão evolutiva dos hospedeiros e, conseqüentemente, mecanismos anti-parasitismo são positivamente selecionados continuamente dentre o conjunto de genes que compõem o genoma do organismo hospedeiro. Entretanto, a seleção positiva de mecanismos anti-parasitismo por parte dos hospedeiros impõe novas pressões seletivas aos organismos parasitas. Dessa maneira, genes de parasitas que permitam o escape dos mecanismos anti-parasitismo do hospedeiro aumentam a aptidão evolutiva do organismo parasita, sendo também selecionados positivamente. Esse fenômeno acaba por causar uma espiral de eventos coevolutivos ao longo do tempo em ambos os genomas no que se refere aos genes envolvidos na relação molecular parasito-hospedeiro. Genes evoluindo sob esse tipo de pressão seletiva no sistema parasita-hospedeiro muitas vezes apresentam uma freqüência de mutações não-sinônimas e sinônimas mais elevada do que a da vasta maioria dos outros genes destes genomas, fenômeno este denominado seleção positiva. Assim, dentre todos os genes observados no genoma de hospedeiros e parasitas, genes sob evidência de seleção positiva são ótimos candidatos a genes envolvidos no relação ecológica de parasitismo. Entretanto, o software existente para o cálculo de seleção positiva é computacionalmente custoso, tornando proibitivo a busca por seleção positiva em escala genômica. Nesse cenário, o presente trabalho descreve um software que faz uso de paralelização para permitir a busca por seleção positiva em escala genômica em tempo exequível.CIIC 2012. No 12612

Utilização da plataforma Galaxy na análise de dados de RNAseq.

Este trabalho teve como objetivo avaliar a plataforma Galaxy na análise de dados de RNA-seq, uma metodologia de sequenciamento de transcritos (moléculas de RNAm) que utiliza as novas tecnologias de sequenciamento (NTS)

POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.

We present POTION, an open source, modular and end-to-end software for genome-scale detection of positive Darwinian selection in groups of homologous coding sequences. Our software represents a key step towards genome-scale, automated detection of positive selection, from predicted coding sequences and their homology relationships to high-quality groups of positively selected genes.X-meeting 2015

Reconstructing the whole mitochondrial DNA (mtDNA) from nuclear genome.

In several eukaryotic organisms, the nuclear genome has several partial copies of the mitochondrial DNA (mtDNA). These copies are called NUMTs (NUclear MiTochondrial DNA) and they have been known since 1967 when the first evidence of them were reported in the mouse nuclear genome. Despite almost fifty years have passed, the reason of their very existence remains controversial. However, their presence has been confirmed in an increasing number of genomes. The NUMts could be only another DNA idiosyncrasy, but they actually represent a serious issue for important application such as genome bar coding. There are many open questions about them.X-meeting 2015

Preliminary analysis of differentially expressed genes involved in meat tenderness in Angus and Nelore beef cattle.

ISCB-Latin America 2014. Pôster O10

Counting RNAseq reads: which way is better?

In this work we show the variation of results we?ve found while working with ~1 billion Illumina reads from drought tolerant Sorghum bicolor genotype in the presence and absence of the stress and compared results found for key genes already characterized.Pôster N101

BDGF: a database and webbased information retrieval system for genotype and phenotype.

In order to get efficient storage and fast queries in this high volume of data, in this work we present the BDGF system (Genotypes and Phenotypes Database). It is based on a data model first proposed by (HIGA, 2015).X-Meeting 2016

Wheat transcriptome analysis targeting leaf rust resistance-related genes.

ISCB-Latin America 2014. Pôster D03

Identification of Schistosoma mansoni microRNAs

Background: MicroRNAs (miRNAs) constitute a class of single-stranded RNAs which play a crucial role in regulating development and controlling gene expression by targeting mRNAs and triggering either translation repression or messenger RNA (mRNA) degradation. miRNAs are widespread in eukaryotes and to date over 14,000 miRNAs have been identified by computational and experimental approaches. Several miRNAs are highly conserved across species. In Schistosoma, the full set of miRNAs and their expression patterns during development remain poorly understood. Here we report on the development and implementation of a homology-based detection strategy to search for miRNA genes in Schistosoma mansoni. In addition, we report results on the experimental detection of miRNAs by means of cDNA cloning and sequencing of size-fractionated RNA samples. Results: Homology search using the high-throughput pipeline was performed with all known miRNAs in miRBase. A total of 6,211 mature miRNAs were used as reference sequences and 110 unique S. mansoni sequences were returned by BLASTn analysis. The existing mature miRNAs that produced these hits are reported, as well as the locations of the homologous sequences in the S. mansoni genome. All BLAST hits aligned with at least 95% of the miRNA sequence, resulting in alignment lengths of 19-24 nt. Following several filtering steps, 15 potential miRNA candidates were identified using this approach. By sequencing small RNA cDNA libraries from adult worm pairs, we identified 211 novel miRNA candidates in the S. mansoni genome. Northern blot analysis was used to detect the expression of the 30 most frequent sequenced miRNAs and to compare the expression level of these miRNAs between the lung stage schistosomula and adult worm stages. Expression of 11 novel miRNAs was confirmed by northern blot analysis and some presented a stage-regulated expression pattern. Three miRNAs previously identified from S. japonicum were also present in S. mansoni. Conclusion: Evidence for the presence of miRNAs in S. mansoni is presented. The number of miRNAs detected by homology-based computational methods in S. mansoni is limited due to the lack of close relatives in the miRNA repository. In spite of this, the computational approach described here can likely be applied to the identification of pre-miRNA hairpins in other organisms. Construction and analysis of a small RNA library led to the experimental identification of 14 novel miRNAs from S. mansoni through a combination of molecular cloning, DNA sequencing and expression studies. Our results significantly expand the set of known miRNAs in multicellular parasites and provide a basis for understanding the structural and functional evolution of miRNAs in these metazoan parasites