CINDEL web server

CINDELDownload ModelUse the Download Model link for the model as this web server runs it.CINDEL is a logistic regression machine learning model for predicting CRISPR–Cas12a/Cpf1 (AsCpf1) guide activity from sequence context.CINDEL provides three analysis modes for CRISPR–Cas12a (Cpf1) guide scoring:

Guide Finder: scan a longer sequence and score all valid TTTV-based 27bp candidates.

Single Sequence: enter a sequence (>= 27 bp), press ENTER to list the 27bp TTTV candidates it holds, pick one from the dropdown, and score it.

Batch Scoring: score many 27bp candidate sequences (one per line), provided as text or as a file.

Input expectations

Valid PAMs are TTTA, TTTG, and TTTC (TTTV, where V is A/G/C).

For Batch Scoring, provide one 27bp candidate sequence per line, either pasted as text or uploaded as a file.

For Guide Finder, nine input formats are supported: FASTA (text or file), Gene Symbol, NMID, Ensembl ID, HGNC ID, Genomic Position, Edit Sequence (an unedited/edited pair), ClinVar ID and COSMIC ID. Each resolves to the sequences the finder scans.

For Single Sequence, enter the sequence directly (text input only — no file upload).

The results page includes an interactive table, score summaries, row-level detail cards, and downloadable output archive.Homology-directed repair (HDR) donor templates. When an input format describes an intended edit — an unedited/edited sequence pair, ClinVar ID or COSMIC ID — the results also carry what each guide needs for HDR: the cut site, the cut-to-edit distance, the donor template in the chosen type and orientation(s) (default: a single-stranded oligo on the sense strand, 100 nt homology arms each side), the realised arm lengths, an optional PAM-blocking mutation, and the candidate's rank among the target's guides. There is no HDR mode switch: the input format decides.Note: DeepCpf1 provides an accurate deep-learning based prediction of Cas12a/Cpf1 guide activity. You might want to use DeepCpf1.

How to run CINDEL

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