Local BLAST Searching in Lasergene
Lasergene applications have long offered integrated sequence similarity and text-based searches using NCBI’s BLAST and Entrez servers. While those resources remain invaluable, not every research environment allows external searches — and not every dataset belongs in the public domain.
With Local BLAST, you can run BLAST searches entirely offline, using databases that you create and manage on your own system. Local BLAST is available in all Lasergene applications that support online BLAST: SeqBuilder Pro, SeqMan Ultra, MegAlign Pro, Protean 3D, and GenVision Pro.
Why do a Local BLAST search?
- Data security and privacy — search proprietary or sensitive sequences without sending them outside your institution.
- Flexibility — create, customize, and maintain your own searchable databases, including both public and proprietary sequence data.
- Performance — internal benchmarks show that local BLAST searches are over 25X faster than searches sent to NCBI, and more than 5X faster than running BLAST directly on the NCBI site
Easy Setup, No IT Skills Required
Traditionally, setting up Local BLAST required downloading and configuring NCBI tools on your own. Lasergene makes this effortless:
- Automatic installation — the NCBI BLAST executables (blastn, blastp, etc.) are installed automatically alongside Lasergene in the “Tools” folder. No extra downloads, paths, or configuration are needed.
- Seamless database setup — when you choose to download an NCBI database (even large ones like nt), Lasergene handles the download and decompression automatically. The database simply appears in your Search UI, ready to use.
- Accessible to everyone — what used to require experienced bioinformatics setup can now be done by any user, right from the application menus.
Key Features of Local BLAST
The Manage Local Databases interface (Search > Manage Local Databases) provides everything you need to build and maintain BLAST-ready databases:
- Download NCBI databases — choose from 30+ databases for automatic download and decompression.
- Import existing BLAST databases — work with databases you’ve already prepared.
- Create new custom databases — build BLAST-ready databases from your own sequence files, including DNASTAR formats like .msa and .sbp.
- Merge multiple databases — combine different sources into a single, comprehensive resource.
- Remove databases — keep your local environment organized.
How Local BLAST Search Works
- Open Search > Manage Local Databases in any supported Lasergene application.
- Download or create the database you want to use — for example, NCBI’s nt database, or a custom dataset like a panel of COVID-19 spike protein sequences.
- When ready to run a search, open the usual Search for Sequences dialog, choose the Local option, and select your preferred database.
- Results are displayed instantly in the familiar Lasergene results table with % Identity, % Coverage, E-values, accession links, maps, alignments, and filtering tools.
Because the search runs locally, even large datasets return results in seconds.
Request a Free Trial or Schedule a Demo with our team to explore how Local BLAST can accelerate your sequence analysis.
