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Bioinformatics

Bindings: %bio.fetch, %bio.sequence, %bio.align, %bio.visualize

A set of interpreters for quick, code-free bioinformatics tasks — no plotting or parsing library required, each just takes plain text and renders a visual result.

%bio.fetch — fetch a structure​

Fetches a 3D structure by a 4-character PDB ID (from RCSB) or a UniProt accession (its predicted structure from AlphaFold DB), and renders it as an interactive 3D molecule viewer.

%bio.fetch
1CRN
%bio.fetch
P69905

%bio.sequence — view a sequence​

Renders a FASTA record (or a bare sequence) as a colored, line-numbered view, detecting nucleotide vs. amino-acid sequences automatically and showing GC content for nucleotide sequences.

%bio.sequence
>my_sequence
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF

%bio.align — align two sequences​

Runs a pairwise (Needleman-Wunsch) global alignment between two sequences, given as raw sequence text or as two UniProt accessions (fetched automatically), and renders the alignment with identity/similarity/gap statistics.

%bio.align
P69905 P68871

%bio.visualize — view a structure file​

Renders a structure file already available to the interpreter (.pdb, .ent, .cif, or .mmcif) as an interactive 3D molecule viewer, given its path.

%bio.visualize
/data/structures/my_protein.pdb

Configuration​

The bioinformatics interpreters have no interpreter-specific properties to configure beyond the common resource/process settings your administrator manages from the interpreter settings screen.