OASIS is a robust, interactive command-line pipeline designed for bioinformatics researchers to effortlessly fetch, align, and strictly filter orthologous sequences from NCBI.
Unlike web-based BLAST searches that query entire databases (introducing noise from paralogs and synthetic sequences), OASIS uses NCBI's evolutionary curation to download true orthologs and applies rigorous dual-filtering thresholds (Identity and Similarity/Positives) to generate highly reliable datasets for multiple sequence alignments (MSA) and phylogenetic analyses.
- Strict Dual-Filtering: Filters orthologs mathematically by both
% Identityand% Similaritysimultaneously. - Molecule Flexibility: Automatically handles both Protein (
NP_,XP_) and Nucleotide (NM_,XM_) queries, adjusting the internal engine (blastporblastx) accordingly. - Sudo-Free (Rootless) Architecture: Perfect for university lab environments. It relies on native Linux tools (
curl/wget,unzip/python3) and installs required bioinformatics tools locally without needing administrator privileges. - Zero-Config Dependencies: Automatically downloads and configures NCBI BLAST+ (v2.13.0) and NCBI Datasets CLI in the user's
$HOMEdirectory. - Batch Extraction: Instantly generates ready-to-use multifasta files for both Proteins and Coding DNA Sequences (CDS).
- Clean Execution: Uses isolated, process-specific temporary directories that self-destruct upon completion or cancellation, leaving your workspace completely clean.
OASIS is designed to run on Linux/Unix-based systems. It requires an active internet connection to query NCBI databases.
Clone this repository and make the script executable:
git clone https://github.com/RodrigoOrvate/OASIS.git
cd OASIS
chmod +x OASIS.shSimply execute the script. It will guide you through an interactive menu:
./OASIS.shWhen you run OASIS, you will be prompted to provide your parameters:
- Accession ID: Provide a valid NCBI RefSeq ID (e.g.,
NP_001416352.1). - Molecule Type: Specify if your query is a Protein (
p) or Nucleotide (n). - Thresholds: Provide the minimum Identity and Similarity percentages (e.g.,
90 95).
Interactive Prompts: After the alignment and filtering steps, OASIS will ask if you want to automatically extract the output files:
- Do you want to extract the protein FASTA file for these sequences? (y/n)
- Do you want to download the nucleotide sequences (CDS) for these orthologs? (y/n)
Depending on your choices, OASIS will generate up to three files in your current directory:
filtered_accessions_ID{min}_SIM{max}_{ID}.txt: A raw text file containing the accession numbers of the orthologs that survived the strict filtering process.sequences_PROT_OASIS_{ID}.fasta: A multifasta file containing the full amino acid sequences for all filtered orthologs.sequences_CDS_OASIS_{ID}.fasta: A multifasta file containing the nucleotide Coding DNA Sequences (CDS) for all filtered orthologs.
OASIS relies on the ncbi-datasets-cli to fetch pre-curated ortholog families. Because of this, it does not accept UniProt IDs (e.g., P09217) or AlphaFold IDs directly.
If you have a UniProt ID, perform an ID Mapping to find its corresponding RefSeq Accession (starts with NP_ or XP_) before running the script.
Don't have access to a Linux terminal? You can run the entire OASIS pipeline directly in your browser using Google Colab. No installation, configuration, or powerful hardware required.
This project is licensed under the MIT License. You are free to use, modify, and distribute this software for academic or commercial purposes, provided that proper credit is given to the original author.
- NCBI Data & Tools: OASIS is an independent, open-source wrapper script. It heavily relies on the NCBI Datasets CLI and BLAST+ executables. This project is not officially affiliated with, maintained, or endorsed by the National Center for Biotechnology Information (NCBI) or the National Institutes of Health (NIH).
- Academic Context: This tool was developed to support computational biology and bioinformatics research initiatives (PIBIC) at the Federal University of Rio Grande do Norte (UFRN).
Developed to streamline rigorous ortholog retrieval for phylogenetic and evolutionary conservation analyses.