FAS2rDNA: From DNA annotation to FASTA-formatted sequence

FAS2rDNA is publicly available

FAS2rDNA is publicly available on GitHub and the instructions for use are completely documented.

About FAS2rDNA

FAS2rDNA is a publicly-available tool for automated, strand-aware reconstruction of DNA sequences from genomic coordinates across multiple reference assemblies, supporting multi-species processing. It is designed for batch, multi-region, and mega-scale workflows in genomics, bioinformatics, and machine learning-driven sequence analysis.

What FAS2rDNA Does

FAS2rDNA simplifies the extraction and reconstruction of DNA sequences by transforming tabulated user data inputs into reconstructed multi-FASTA outputs. Given genomic coordinates, FAS2rDNA automatically retrieves reference genomes and reconstructs the corresponding DNA sequences in a reproducible and deterministic manner. The tool is optimized for large datasets where manual sequence extraction or ad hoc scripting becomes inefficient, error-prone, or non-reproducible.

Why FAS2rDNA Matters

Modern genomics is no longer limited by data generation, but by how efficiently genomic information can be transformed into machine-usable representations. As sequencing projects scale to millions of regions and thousands of samples, reproducible and automated sequence reconstruction becomes a critical bottleneck. FAS2rDNA addresses this gap by providing a deterministic, genome-scale bridge between coordinate-based genomic data and sequence-level analysis—enabling downstream applications in large-scale genomics, machine learning, and AI-driven biological modeling.

How to Use FAS2rDNA

FAS2rDNA works both in local and cloud-based implementations.
1. CLI version: Designed for high-performance and production-scale workflows.

• Intended for local machines, servers, and HPC environments

• Supports large batch jobs and automation

• Ideal for pipelines, reproducible research, and integration with downstream tools

Learn more here: https://github.com/mahvin92/FAS2rDNA

2. Colab version: Designed for accessibility, teaching, and rapid prototyping.

• Runs entirely in the browser

• No local setup required

• Ideal for demonstrations, tutorials, and exploratory analysis

Learn more here: https://github.com/mahvin92/FAS2rDNA-Colab

Publications

FAS2rDNA-Colab: A cloud-based workflow for pan-cancer, isoform-wide miRNome reconstitution across TCGA cohorts. Protocols.io (2025). DOI: 10.17504/protocols.io.14egn1xr6v5d/v1

High-throughput isoform-wide miRNome sequence reconstruction in the TCGA-LUAD cohort using FAS2rDNA. Protocols.io. (2025). DOI: 10.17504/protocols.io.rm7vzenqxvx1/v1