{"doi":"10.1101/2025.04.13.648579","title":"TD2: finding protein coding regions in transcripts","abstract":"ABSTRACT The transcriptome encompasses all RNA transcripts in eukaryotic cells, orchestrating gene expression and regulating cellular function, development, and adaptation. Identifying open reading frames (ORFs) in transcripts is a critical step in transcriptome analysis. We introduce TD2, a new tool for ab initio annotation of protein-coding ORFs in transcripts. We find TD2 to be sensitive and precise when compared to other state-of-the-art tools in reference transcripts and transcriptome assemblies from a diverse array of eukaryotes. TD2 is available at https://github.com/Markusjsommer/TD2 . The project is open-source, developed in Python with PyTorch, and is freely available to all academic, government, and commercial users under the MIT license.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":554975,"datarank":0.26876392038420827,"base_score":1.791759469228055,"endowment":1.791759469228055,"self_citation_contribution":0.26876392038420827,"citation_network_contribution":0.0,"self_endowment_contribution":0.26876392038420827,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9517,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1138479,"name":"Hyun Joo Ji","orcid":"0009-0008-4360-5428","position":1,"is_corresponding":false},{"id":29096,"name":"Brian J. Haas","orcid":"0000-0002-6609-4973","position":2,"is_corresponding":false},{"id":4334,"name":"Steven L. Salzberg","orcid":"0000-0002-8859-7432","position":3,"is_corresponding":false},{"id":693941,"name":"Markus J. Sommer","orcid":"0000-0003-3414-1875","position":4,"is_corresponding":false},{"id":890166,"name":"Alan Mao","orcid":"0000-0003-2381-0607","position":0,"is_corresponding":true}],"reference_count":17,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:54:54.542303Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}