BLAST

BLAST finds sequences similar to a query by aligning it against biological databases and scoring the matches for statistical significance. Reach for it in structure work to identify homologs of your protein — related sequences whose known structures or annotations you can borrow, or whose top hit you can fold. It is a search step that feeds the folding tools rather than producing structures itself: pair it with ESMFold to fold a hit, or AlphaFold and the PDB to look one up. See what you can achieve for the full set.

BLAST (Basic Local Alignment Search Tool) is the gold standard for biological sequence similarity searching. Developed by NCBI, BLAST compares nucleotide or protein sequences against databases to identify similar sequences and calculate statistical significance.

Citations

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of Molecular Biology. 1990 Oct 5;215(3):403-10. doi: 10.1016/S0022-2836(05)80360-2

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009 Dec 15;10:421. doi: 10.1186/1471-2105-10-421

NCBI BLAST: https://blast.ncbi.nlm.nih.gov

Recent updates (2024)

• ClusteredNR: The default database for protein BLAST searches is transitioning to NCBI ClusteredNR, built from protein sequence clusters
• Core nucleotide (core_nt): An alternative to the default nt database that is more compact and efficient—less than half the size

Beyond the hosted search, these guides cover BLAST+ command lines — remote searches, preparing databases, and repeatable batch runs with clean outputs. You can ask Ivy to run them in the chat's code workspace, which ships BLAST+, or run them on your own machine.

Chat Usage

Example Prompts

• "Run BLAST on this protein sequence against SwissProt"
• "Search for homologs of human insulin in the PDB database"
• "BLAST this sequence and fold the top hit with ESMFold"

Workflow Chaining

• Feeds into: ESMFold (fold hit sequences), Target Passport (identified targets), UniProt (annotation lookup)
• Accepts from: UniProt (sequences), ESMFold (query protein identity)

FAQ

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