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### Puffin Prediction (`puffin-prediction`) Runs a single forward pass through Puffin and returns per-base predictions across all 10 transcription-initiation channels (5 assays × 2 strands) at single-base resolution. #### API Reference

Source DNA sequence(s) at least 651 bp long. A single string is normalized to a one-item list. Only `A`, `C`, `G`, `T`, `N` are accepted.

Source Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device used for inference. 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 Per-sequence prediction results. Input DNA sequence that was scored. Length of the input sequence. Number of per-base output positions (= `sequence_length - 650`). 0-based sequence coordinate of the first per-base output position (always `325`). 0-based exclusive end of the per-base output span in the input sequence (= `sequence_length - 325`). Per-base predictions with shape `[output_length, 10]`. Channel order matches `TRACK_NAMES`. Names of the 10 output channels in order.

#### Applications Use this tool to score transcription start sites, rank candidate promoters, or measure the per-base effect of variants and edits across five capped-5'-end assays in one call. The fast path is the right choice when the question is *how much* signal a sequence produces rather than *why*. #### Usage Tips * **Per-base output length is `len(sequence) - 650`.** The model uses 325 bp of padding on each side; output coordinates run from 325 to `len(sequence) - 325` in the input frame. * **Channel order is mirrored across strands.** The first 5 channels are FANTOM\_CAGE+ → PRO\_CAP+; the next 5 are PRO\_CAP- → FANTOM\_CAGE-. Index by name via `TRACK_NAMES.index(...)` rather than memorizing positions. * **Outputs are in log scale.** Treat predicted values as `ln(count_scale_signal + 1)`. To compare two sequences, subtract — the difference is already in log space.

### Puffin Interpretation (`puffin-interpretation`) Runs Puffin's gradient-based decomposition for one chosen target assay and strand. Returns the per-base prediction for that target, 18 motif-activation tracks, 18 motif-effect tracks, and per-base basepair-contribution scores both as an aggregate and decomposed two ways (contribution to the predicted signal per motif, and contribution to each motif's activation per basepair; 18 tracks each). Summed motif, initiator, trinucleotide, and total-effect tracks are also returned. #### API Reference

Source DNA sequence(s) at least 651 bp long. A single string is normalized to a one-item list. Only `A`, `C`, `G`, `T`, `N` are accepted.

Source Which transcription initiation assay's predictions to decompose into motif and basepair contributions. Available options: `FANTOM_CAGE`, `ENCODE_CAGE`, `ENCODE_RAMPAGE`, `GRO_CAP`, `PRO_CAP` If `True`, decompose the reverse-strand prediction for the chosen target instead of the forward strand. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device used for inference. 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 Per-sequence interpretation results. Input DNA sequence that was scored. Length of the input sequence. Number of per-base output positions (= `sequence_length - 650`). 0-based sequence coordinate of the first per-base output position (always `325`). 0-based exclusive end of the per-base output span in the input sequence (= `sequence_length - 325`). Predicted transcription initiation signal for the selected `target_signal` and strand, length `output_length`. Per-base motif activation scores keyed by strand-suffixed motif name (e.g. `"TATA+"`). Per-base motif effect scores keyed by strand-suffixed motif name. Per-base sum of motif effects across non-initiator motifs. Per-base sum of initiator-motif effects (centered to zero mean). Per-base sum of trinucleotide sequence effects (centered to zero mean). Per-base sum of all sequence pattern effects (motif + initiator + trinucleotide). Per-base contribution score to transcription initiation at the target. Per-base contribution to transcription, decomposed by motif name. Per-base contribution to motif-activation scores, decomposed by motif name. Target signal selected for interpretation. Whether the reverse-strand head was used. The 9 learned motif names (without strand suffix) exposed in the per-motif tracks. Strand-suffixed names appear as keys in each result's motif-keyed dicts.

#### Applications Use this tool to ask which motif drives a transcription start site, how a variant changes a motif activation, or how initiator and trinucleotide context shape the predicted signal. It is substantially slower than `puffin-prediction` because it computes per-base gradient contributions, so reach for it for mechanistic follow-up on specific sequences rather than for bulk scoring. #### Usage Tips * **`target_signal` picks which assay's prediction is decomposed.** Choose the one closest to the biological question; CAGE/RAMPAGE measure capped mRNA 5' ends, while GRO-cap/PRO-cap measure nascent transcription. * **`reverse_strand` selects which strand head to interpret.** Defaults to forward; run it twice on the same input to analyze divergent or antisense promoters. * **Motif dicts use strand-suffixed keys.** Access `motif_activations["TATA+"]` and `motif_activations["TATA-"]`, never the bare motif name. `MOTIF_NAMES` lists the 9 motif stems.