Author Archives: hugorody

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

Posted in Local Tools | Leave a comment

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

Posted in Local Tools | Leave a comment

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

Posted in Blog | Tagged , | Leave a comment

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

Posted in Blog | Leave a comment

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

Posted in Blog | Leave a comment

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! https://github.com/quinlan-lab/applied-computational-genomics

Posted in Blog | Leave a comment

Both mechanism and age of duplications contribute to biased gene retention patterns in plants

In general, transcription factor (GO:003700) paralogs tend to be overrepresented amongst ancient (Ks > 1) duplication regardless of mechanism of duplication. RESEARCH ARTICLE – https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3423-6 – https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5219802/

Posted in Blog | Leave a comment