Silva rRNA and Human RNA BLAST Database for Visium Probe Design

A BLAST database contains Silva LSU and SSU rRNA sequences (version 138.2), the human transcriptome, and human tRNAs. It was created by author Chia, Minghao using BLAST version 2.12.0 and is paired with NCBI genome metadata for running the visium_probe_design_nf pipeline. The dataset was last updated on 2026-06-24.

Use Cases

• Designing spatial transcriptomics probes based on rRNA and transcriptome sequences.
• Running BLAST searches against a combined microbial and human RNA database.
• Downloading reference genomes from NCBI using the provided metadata file.

Strengths

• Includes specific Silva rRNA database version 138.2.
• Created with a defined software tool (BLAST v2.12.0).
• Directly supports a specific, linked GitHub pipeline for probe design.

Limitations

• Description metadata is limited; actual data quality requires manual inspection after download.
• Column-level documentation is absent; field semantics must be inferred after download.
• Row count and file size are unknown, which may limit suitability assessment.

Provenance

Source

Minghao Chia visium_probe_design_nf

Collection Method

Made using BLAST (v2.12.0), and compressed with 7zip.

Freshness

Last updated 2026-06-24 02:52:18; freshness should be verified.