FAS2rDNA-Colab

Colab-friendly implementation of FAS2rDNA.

FAS2rDNA is a lightweight, assembly‑aware reconstruction engine that converts genomic coordinates and annotations into multi-FASTA sequences. It supports short fragments to large regions (genes, isoforms, loci) across multiple species and assemblies, using a simple tabular input format that is optimized for downstream analytics and machine learning workflows.

Links:

Launch FAS2rDNA-Colab on Google Colaboratory

Read the protocol here: Protocols.io

Visit the official wesite here: FAS2rDNA by ChordexBio

FAS2rDNA-Colab Usage

1. Preparing your data

a. Data format:

i) Obtain and compile your genomic annotations and coordinates in a table and format your columns to contain the following column headers:

• sample_id: the identifier of your sample (e.g., sample source)
• seq_loc: the genomic coordinate of your sequence (see below for standards)
• seq_id: the identifier of the sequence (e.g., gene name)
• description: any information about the sequence entry

Table 1. Sample data format.

sample_id	seq_loc	seq_id	description
BLOOD_001	hg19:9:106938220-106938244:+	TP53	Tumor protein p53; genomic locus on chromosome 17.
LIVER_A2	hg38:11:86938550-86938664:-	BRCA2	DNA repair protein; captured via targeted enrichment.
SKIN_NS	hg18:7:96998253-97038145:+	BRAF	Proto-oncogene; wild-type sequence from control group.
BONE_M	hg19:1:76938211-76949381:-	NRAS	Neuroblastoma RAS viral oncogene homolog.

- Note that you can have additional headers as long as you have all the required column headers, listed above.

ii) Save your file in a tab-delimited text file (.txt or .tsv). File --> Save As ---> TXT or TSV --> Save

b. Standard genomic coordinate:

The seq_loc field MUST assume ONLY the following format: genome_assembly:chromosome_number:DNA_location:strand_location, as shown in the Figure 1 below:. For example, the coordinate 'hg19:9:106938220-106938244:+' (as exemplified in Table 1) is to be reconstructed using the hg19 genome assembly, chromosome 9, DNA locations 106938220-106938244 nt, in the positive sense strand.

Figure 1. Standard format for the genomic coordinate in column seq_loc of your data.

2. Performing a multi-FASTA reconstruction

a. Launching the software:

The FAS2rDNA-Colab can be opened in several ways:

i) Launch from the shareable link here: FAS2rDNA-Colab

ii) Download the FAS2rDNA-Colab notebook from the ipynb folder on GitHub/FAS2rDNA-Colab and manually upload that in your Colab workspace File --> Upload Notebook.

iii) Load FAS2rDNA-Colab directly from an opened Colab notebook by running the code below:

from IPython.display import HTML

notebook = "FAS2rDNA-colab_v1_0.ipynb" # -> change the version here
repo = "mahvin92/FAS2rDNA-Colab"
folder = "ipynb"

colab_url = f"https://colab.research.google.com/github/{repo}/blob/main/{folder}/{notebook}"
HTML(f'<a href="{colab_url}" target="_blank">Open {notebook} in Google Colab</a>')

b. Running FAS2rDNA-Colab

i) Type the name of your experiment in the Project_name field

ii) Click Runtime and select Run all

iii) Upload your files by clicking Choose Files below the cell block in Step 1. Upload data

iv) Wait for the run to complete

v) Results will be automatically downloaded or manually get them from /content/fas2rdna/outputs

c. Validating the results

FAS2rDNA-Colab returns two types of data:

i) the individual .fasta file from multiple txt inputs

ii) the combined .fasta file, compiling all multi-FASTA sequences in one file.

Sample result:

>BLOOD_001
AAATCGGCGGACTCGGCAC ...
>LIVER_A2
TTTAAACGCCCCCACGCCT ...
>SKIN_NS
GGGCGCGTTACGTGCACGT ...
>BONE_M
TGCATTGACACCACTTCGG ...

Supported Assemblies

The following genome assemblies are currently supported in the v.1.0 of FAS2rDNA-Colab (FAS2rDNA will detect them automatically). For more information, please refer to: UCSC Genome Browser.

• Human: hg16, hg17, hg18, hg19, hg38, hs1
• Mouse: mm7, mm8, mm9, mm10, mm39
• Rat: rn4, rn5, rn6, rn7
• Zebrafish: danRer7, danRer10, danRer11
• Fruit Fly: dm2, dm3, dm6
• C. elegans: ce4, ce6, ce10, ce11
• Yeast (S. cerevisiae): sacCer1, sacCer2, sacCer3

Troubleshooting

1. No FASTA output generated

• Verify that output directories exist, unchanged, and all cells/steps are sequentially executed.
• Confirm that the seq_loc column exists in your data and all assemblies referenced in are supported or validated
• Refresh your File browser to force Colab to load your files

2. FAS2rDNA is skipping entries

• Confirm that those entries contain a valid and well-formatted seq_loc data

3. Empty or truncated sequences

• Check coordinate validity (start < end, within chromosome bounds)
• Ensure reference FASTA files are complete and indexed

4. Incorrect strand orientation

• Confirm the strand field in seq_loc is correctly specified as + or -

5. Performance bottlenecks with large datasets

• Enable chunked writing or parallel execution
• Split input files by chromosome or sample batches

Reporting

Comments and suggestions to improve FAS2rDNA-Colab are welcome. If you find any bug or problem, please open an issue.

Citation

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

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

Acknowledgement

FAS2rDNA-Colab is powered by ChordexBio, FAS2rDNA and CodeEnigma, made with Python, and tested using Google Colab ❤️