Author Archives: hugorody

Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype

New manuscript on BMC Genomics. Link here! Background Resistance genes composing the two-layer immune system of plants are thought as important markers for breeding pathogen-resistant crops. Many have been the attempts to establish relationships between the genomic content of Resistance … Continue reading

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Making OrthoMCL easier to use

“OrthoMCL is an algorithm for grouping proteins into ortholog groups based on their sequence similarity. “ With more than 3K citations, the OrthoMCL elegantly finds orthologs, co-orthologs, and in-paralogs in protein FASTA files. If all that you need is to … Continue reading

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NJ trees for multiple FASTA files using Phangorn R package

This script intends to iterate with multiple-sequence alignment (MSA) FASTA files in a directory and create Neighbor-Joining (NJ) trees for each of those files. For this, we will use R and the package Phangorn. Phangorn is described as a package … Continue reading

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Brief comparison of NGS platforms

Short reads (SBL and SBS types) SBL – Sequencing by ligation type Solid [50-75 bp] (80-320 Gb) BGISEQ [50-100 bp] (8-200 Gb) SBS – Sequencing by synthesis type (CRT Cycle Reversible Termination) Illumina [25-300 bp] (540 Mb – 900 Gb) … Continue reading

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Evolutionary history of the cobalamin-independent methionine synthase gene family across the land plants

Plants are successful paleopolyploids. The wide diversity of land plants is driven strongly by their gene duplicates undergoing distinct evolutionary fates after duplication. We used genomic resources from 35 model plant species to unravel the evolutionary fate of gene copies … Continue reading

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I Curso de Inverno em Bioinformática UNIFESP

The first Winter School of Bioinformatics of Institute of Science and Technology of the Federal University of São Paulo (ICT-Unifesp) will be holden next july 10 to 12. The speakers are linked to the Biocomputational Project – fomented by CAPES … Continue reading

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Applied Computational Genomics Course at UU, Aaron Quinlan

Professor Aaron Quinlan (University of Utah), author of BEDtools (link1, link2), has published his “Applied Computational Genomics Course at UU: Spring 2017”. Highly recommended!

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