{"doi":"10.1093/bioinformatics/btab247","title":"tSFM 1.0: tRNA Structure–Function Mapper","abstract":"MOTIVATION: Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their evolutionary divergences. Although permutation P-values can quantify the significance of CIF divergences between two taxa, their naive Monte Carlo approximation is slow and inaccurate. The Peaks-over-Threshold approach of Knijnenburg et al. (2009) promises improvements to both speed and accuracy of permutation P-values, but has no publicly available API. RESULTS: We present tRNA Structure-Function Mapper (tSFM) v1.0, an open-source, multi-threaded application that efficiently computes, visualizes and assesses significance of single- and paired-site CIFs and their evolutionary divergences for any RNA, protein, gene or genomic element sequence family. Multiple estimators of permutation P-values for CIF evolutionary divergences are provided along with confidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI. AVAILABILITY AND IMPLEMENTATION: The data underlying this article are available on GitHub at https://github.com/tlawrence3/tSFM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","journal":"Bioinformatics","year":2021,"id":224052,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9522,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":403452,"name":"Fatemeh Hadi-Nezhad","orcid":null,"position":1,"is_corresponding":false},{"id":825813,"name":"Ivo Große","orcid":"0000-0001-5318-4825","position":2,"is_corresponding":false},{"id":402310,"name":"David H. Ardell","orcid":"0000-0001-7313-0963","position":3,"is_corresponding":false},{"id":402309,"name":"Travis J. Lawrence","orcid":"0000-0002-7380-489X","position":0,"is_corresponding":true}],"reference_count":21,"raw_metadata":null,"created_at":"2026-07-18T23:54:14.760456Z","pmid":"33904572","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":[]}