Estimating Sequence Similarity from Read Sets for Clustering Sequencing Data

Conference paper

DOI: 10.1007/978-3-319-46349-0_18

Volume 9897 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Ryšavý P., Železný F. (2016) Estimating Sequence Similarity from Read Sets for Clustering Sequencing Data. In: Boström H., Knobbe A., Soares C., Papapetrou P. (eds) Advances in Intelligent Data Analysis XV. IDA 2016. Lecture Notes in Computer Science, vol 9897. Springer, Cham


Clustering biological sequences is a central task in bioinformatics. The typical result of new-generation sequencers is a set of short substrings (“reads”) of a target sequence, rather than the sequence itself. To cluster sequences given only their read-set representations, one may try to reconstruct each one from the corresponding read set, and then employ conventional (dis)similarity measures such as the edit distance on the assembled sequences. This approach is however problematic and we propose instead to estimate the similarities directly from the read sets. Our approach is based on an adaptation of the Monge-Elkan similarity known from the field of databases. It avoids the NP-hard problem of sequence assembly and in empirical experiments it results in a better approximation of the true sequence similarities and consequently in better clustering, in comparison to the first-assemble-then-cluster approach.


Read sets Similarity Hierarchical clustering 

Copyright information

© Springer International Publishing AG 2016

Authors and Affiliations

  1. 1.Department of Computer Science, Faculty of Electrical EngineeringCzech Technical University in PraguePragueCzech Republic