Motif Scan
seq_motif_scanRead-onlyIdempotent
Scan nucleotide sequences for IUPAC motif occurrences, supporting ambiguous bases and bracket groups. Control overlapping match reporting with a simple parameter.
Instructions
Scan a nucleotide sequence for IUPAC motif occurrences (supports bracket groups).
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| motif | Yes | IUPAC motif to search for, optionally with bracket groups (e.g. 'ATG[AC]' matches ATGA and ATGC). Valid: A,C,G,T,U,R,Y,S,W,K,M,B,D,H,V,N. | |
| sequence | Yes | Nucleotide sequence (DNA or RNA; case-insensitive). IUPAC ambiguity codes (R, Y, S, W, K, M, B, D, H, V, N) are accepted where documented. | |
| max_matches | No | Cap on the number of matches reported. When the cap is reached the result's truncated flag is True and the reported matches are a prefix; narrow the motif or set overlapping=False for the full set. | |
| overlapping | No | If True, report overlapping matches (next scan starts at the next base); if False, scan greedily left-to-right. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| motif | Yes | The motif searched for (uppercased). | |
| matches | Yes | Match positions (empty when the motif is not found). | |
| sequence | Yes | The input nucleotide sequence (uppercased). | |
| truncated | No | True when the match cap (max_matches) was reached and the reported matches are a prefix of the full result set. Narrow the motif or set overlapping=False to get all matches. |