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### MEME FIMO Motif Scan (`meme-fimo-scan`) Scans one or more target sequences against every position weight matrix in a MEME-format motif file and returns each occurrence with its motif id, 1-indexed coordinates, strand, log-odds score, p-value, and q-value. #### API Reference

Source Target sequences to scan for motif occurrences. A single sequence string is normalized to a one-element list. Path to a MEME-format motif file (`.meme`) of position weight matrices, e.g. exported from JASPAR. `AssetRef` supported.

Source Report only matches with a p-value at or below this cutoff (FIMO `--thresh`). Default 1e-4. Scan both the given and reverse-complement strands. Set False for single-strand scans (FIMO `--norc` disables the reverse strand). Automatically ignored for protein / non-complementable motifs, which are always scanned forward-only. Default True. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source One entry per input sequence, positionally aligned to `MEMEFimoScanInput.sequences` — `results[i]` holds the matches found in sequence `i` (empty if none). Occurrences in this sequence, across all motifs.

#### Applications Use this when the question is "where does motif X occur in these sequences." Typical workflows include locating transcription-factor binding sites in promoters or enhancers, screening a designed regulatory library for unwanted or intended motif occurrences, and annotating candidate sites for downstream filtering on score or q-value. #### Usage Tips * **`threshold` is the p-value cutoff and is the main sensitivity parameter.** It defaults to `1e-4`, reproducing FIMO's command-line default (`--thresh`); only matches with a p-value at or below this value are reported. Loosen it (e.g. `1e-3`) to recover weaker sites at the cost of more false positives, or tighten it for stringent calls. The reported q-value gives the false discovery rate for filtering after the scan. * **`both_strands` controls strand coverage for nucleotide motifs.** It defaults to `True`, scanning the forward strand and its reverse complement (the right choice for DNA/RNA motifs, which can bind on either strand). Set it to `False` for single-strand scans (this maps to FIMO's `--norc`). For protein and other non-complementable motifs the reverse complement is meaningless, so it is ignored automatically and scanning is always forward-only — matching the FIMO CLI. * **Motifs come from MEME-format files, such as those exported from JASPAR.** Supply a `.meme` PWM file; matrices from JASPAR and other databases can be converted to this format. The scan iterates over every motif in the file against every target sequence.