biostudies-literatureUnknown36(10)Perovic V<h4>Motivation</h4>Proteins containing tandem repeats (TRs) are abundant, frequently fold in elongated non-globular structures and perform vital functions. A number of computational tools have been developed to detect TRs in protein sequences. A blurred boundary between imperfect TR motifs and non-repetitive sequences gave rise to necessity to validate the detected TRs.<h4>Results</h4>Tally-2.0 is a scoring tool based on a machine learning (ML) approach, which allows to validate the results of TR detection. It was upgraded by using improved training datasets and additional ML features. Tally-2.0 performs at a level of 93% sensitivity, 83% specificity and an area under the receiver operating characteristic curve of 95%.<h4>Availability and implementation</h4>Tally-2.0 is available, as a web tool and as a standalone application published under Apache License 2.0, on the URL https://bioinfo.crbm.cnrs.fr/index.php? route=tools&tool=27. It is supported on Linux. Source code is available upon request.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.Bioinformatics (Oxford, England)3260-3262https://www.ebi.ac.uk/biostudies/studies/S-EPMC7214015biostudies-literatureTally-2.0: upgraded validator of tandem repeat detection in protein sequences.PMC7214015Veljkovic NSumonja NRichard FDKajava AVLeclercq JYPerovic VfalseTally-2.0: upgraded validator of tandem repeat detection in protein sequences.<h4>Motivation</h4>Proteins containing tandem repeats (TRs) are abundant, frequently fold in elongated non-globular structures and perform vital functions. A number of computational tools have been developed to detect TRs in protein sequences. A blurred boundary between imperfect TR motifs and non-repetitive sequences gave rise to necessity to validate the detected TRs.<h4>Results</h4>Tally-2.0 is a scoring tool based on a machine learning (ML) approach, which allows to validate the results of TR detection. It was upgraded by using improved training datasets and additional ML features. Tally-2.0 performs at a level of 93% sensitivity, 83% specificity and an area under the receiver operating characteristic curve of 95%.<h4>Availability and implementation</h4>Tally-2.0 is available, as a web tool and as a standalone application published under Apache License 2.0, on the URL https://bioinfo.crbm.cnrs.fr/index.php? route=tools&tool=27. It is supported on Linux. Source code is available upon request.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.2020-01-01T00:00:00Z2020 May2022-02-09T18:05:03.851Z2022-02-09T18:05:03.851ZS-EPMC72140153209682010.1093/bioinformatics/btaa121