Phylogenomic study of pcNAT sequences in plant database

Project information

This is a data mining project relate to NATs (natural antisense transcripts). NATs are important regulators of gene expression. We investigate the putative coding NATs associated to lignin biosynthesis in different available database of plants. Homologous of 46 lignin-related genes of Zea mays (INPUT) in 71 organisms available in Ensembl Compara Database were used as target to find and quantify putative protein coding NATs (Natural Antisense Transcripts) based on cDNA public data.

tools used in this script: Ensembl Compara database API + seqkit + ORFFinder

Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.

pcNAT metagenomics ensemble seqkit ORFFinder