Tally-2.0: upgraded validator of tandem repeat detection in protein sequences.

Vladimir Perovic, Jeremy Y Leclercq, Neven Sumonja, Francois D Richard, Nevena Veljkovic, Andrey V Kajava

Bioinformatics (Oxford, England) 2020 May 01

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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. 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%. 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. Supplementary data are available at Bioinformatics online. © The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Citation

Vladimir Perovic, Jeremy Y Leclercq, Neven Sumonja, Francois D Richard, Nevena Veljkovic, Andrey V Kajava. Tally-2.0: upgraded validator of tandem repeat detection in protein sequences. Bioinformatics (Oxford, England). 2020 May 01;36(10):3260-3262