Running Per-Sequence Searches on NCBI Using Web BLAST in Constellab

🔍 Introduction

This task wraps NCBI’s web BLAST service to run per-sequence remote BLAST directly from Constellab. It automatically splits your FASTA into single-sequence queries, submits them to NCBI, waits politely between requests, and collects results as clean .tsv tables one per query. Use it when you want up-to-date results against NCBI’s online databases without maintaining local BLAST databases.

🧰 Prerequisites

• Access to Constellab and a valid Digital Lab environment

• Installed bricks: gws_omix ≥ 0.11.11
• A FASTA file (nucleotide or protein)

🧪 Workflow: Step by Step

1. Add the task: Choose NCBI web BLAST in Constellab.
2. Provide input: Link your input_fasta.
3. Configure parameters: Choose blast_program consistent with your sequence type: blastn → sequence_type=nuclblastp → sequence_type=protblastx → sequence_type=nucl (nucl query vs protein DB) tblastn → sequence_type=prot (prot query vs translated nucl DB)Select sequence_type: "nucl" (nucleotide) or "prot" (protein). Set evalue (e.g., 1e-5 for stricter matches). Set max_target_seqs (e.g., 5–50 depending on breadth vs precision).
4. Run the task

📤 Output

  NCBI web BLAST task produces a blast_results ResourceSet containing one .tsv file per query sequence. Each table includes: