scan_splice_sites
Find the splice sites a sequence accidentally spells - the check a codon-optimised CDS needs before it goes into a plant or any other eukaryotic host, because a synonymous swap chosen for codon usage or GC can spell a donor or acceptor that was not there before, and the transcript is then spliced somewhere nobody intended. Every GT and AG is scored two ways that are NOT on one scale and are never combined: maxEnt is strength under Yeo & Burge's published maximum-entropy model, and typicality is log-odds against base frequencies MEASURED at the annotated splice sites of Arabidopsis thaliana TAIR10 (Ensembl Plants 63). IT RETURNS NO VERDICT and has no default threshold: neither model publishes a cutoff, so this RANKS candidates and what counts as dangerous is your call, with both numbers in front of you.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| strand | No | which strand to read. Both by default: an antisense site still splices a transcript made from the other strand, and in a construct both may be transcribed. Name the gene's own strand when you know it, and the other strand's candidates stop crowding the ranking. | both |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| sequence | No | the DNA to scan - leave unset to use the open record. | |
| min_maxent | No | report only sites at or above this MaxEntScan score, in bits. UNSET BY DEFAULT and deliberately so - MaxEntScan publishes no significance cutoff and the measured matrices are a description rather than a classifier, so a default here would be a decision boundary nobody has published. Set it when you have a threshold of your own. In bits. | |
| max_results | No | how many to return, strongest first. Advanced. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| count | Yes | how many are reported | |
| sites | Yes | the candidates, strongest MaxEnt first, each with its kind, position on the strand you passed, the window that was scored, and both scores | |
| strongest | Yes | the highest-scoring candidate, or null when the sequence is too short to hold a window | |
| strongestMaxEnt | Yes | that candidate's MaxEntScan score on its own, for a comparison downstream, or null when there is no candidate: 0 is a real MaxEntScan score |