BLAST WASM

BLAST is a sequence search and alignment tool used in bioinformatics. It's one of the best-known and most important programs in the field.

Given the query sequence, the BLAST algorithm returns/finds the closest matching sequences in a sequence database. The output of a BLAST search is a list of (sub)sequences from the database with the corresponding E-values.

The BLAST source code is written in C++ and is part of the NCBI C++ Toolkit. The toolkit includes five main BLAST programs (blastn, blastp, blastx, tblastn, and tblastx) plus other utilities and libraries.

I've compiled BLAST programs to WebAssembly using Emscripten to make a version of each program that can run fully in the browser (see the demo below). The NCBI C++ Toolkit codebase is large and complex and required some modifications to compile with Emscripten.

The demo runs makeblastdb to create a BLAST database and then blastp to do a BLAST search against the database. The demo is interactive, so you can change the input sequences and see the results in real-time.

Demo: In-browser BLAST (makeblastdb + blastp)

See also

• WebLogo in the browser - Bringing WebLogo to the browser + demo of a pure client side sequence logo maker.
• DESeq2 in the browser - Running DESeq2 in the browser.
• Sequence Logo Generator - Create sequence logos from FASTA alignments.
• Genome Browser - Explore the human genome.
• Sequence Alignment Viewer - Open FASTA files in the browser.
• Phylogenetic Tree Editor - An online visual editor for phylogenetic trees (WIP).
• Phylogenetic Tree Builder - Reconstruct phylogenetic trees from protein or DNA/RNA sequence alignments.
• Plasmid Map Generator - A tool to generate plasmid maps from GenBank files.
• WikiPathways: A Wikipedia for biological pathways - An overview of the collaboratively edited structured pathway encyclopedia.
• The RDF model of the Gene Ontology, demystified - An outline of the structure of the Gene Ontology RDF graph and ways to query it.
• The ambitious challenge of finishing the human genome - Generating a complete human genome sequence, chromosome by chromosome.
• Scalable genomic alignment with Progressive Cactus - How progressive alignment makes it possible to efficiently align hundreds to thousands of large genomes.
• GenBank to FASTA - Convert GenBank flat files to FASTA format.
• ABI to FASTA - Convert AB1 files (Applied Biosystems/ABI trace files) to FASTA format.
• Awesome bioinformatics - A curated list of awesome resources on bioinformatics.
• NCBI Taxonomy Browser - A simple tool for viewing the NCBI taxonomy tree.
• What is FASTA and how is it used? - Learn about the FASTA format and its applications.
• FASTA Editor - A FASTA editor for creating and editing FASTA files.
• FASTA Parse Tree Viewer - Visualize the parse tree of FASTA files.
• FASTQ to FASTA Converter - Convert FASTQ files to FASTA format.
• FASTQ Editor - A FASTQ editor for creating and editing FASTQ files.
• Newick Editor - An online editor for phylogenetic trees in the Newick format.
• Newick Parse Tree Viewer - View the parse trees of Newick strings.
• PDB Editor - Edit PDB files online.
• PDB to FASTA - Extract protein/nucleotide sequences from PDB files.
• Bioinformatics Crossword - A daily crossword puzzle for bioinformatics terms.
• Bioinformatics pronunciation guide - A pronunciation guide for bioinformatics terms.
• RDKit WASM - Running RDKit in the browser with WebAssembly.
• Phonetic Analyzer - A web-based phonetic analyzer built on top of Praat.
• Font Parser - An online tool for parsing font files.
• FreeType WASM - A WASM port of the FreeType library.
• WASM WAT Editor - A simple editor for the WebAssembly Text Format (WAT).
• WASM ports - A list of software compiled to/ported to WebAssembly/JavaScript.
• Awesome WebAssembly - A curated list of awesome resources on WebAssembly (WASM).
• Erlang/OTP WASM (Erlang in the browser) - Execute Erlang code in the browser.