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ORFFinder

OrfFinder is a Python tool that efficiently identifies Open Reading Frames (ORFs) in DNA sequences. By using suffix arrays and the Longest Prefix Suffix (LPS) algorithm, it searches for specified start and end patterns within a genome. This project is designed for bioinformaticians and researchers who need a fast and reliable method to locate ORFs in genomic data.

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.