Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions

Duplicate sequence records-that is, records having similar or identical sequences-are a challenge in search of biological sequence databases. They significantly increase database search time and can lead to uninformative search results containing similar sequences. Sequence clustering methods have been used to address this issue to group similar sequences into clusters. These clusters form a nonredundant database consisting of representatives (one record per cluster) and members (the remaining records in a cluster). In this approach, for nonredundant database search, users search against representatives first and optionally expand search results by exploring member records from matching clusters. Existing studies used Precision and Recall to assess the search effectiveness of nonredundant databases. However, the use of Precision and Recall does not model user behavior in practice and thus may not reflect practical search effectiveness. In this study, we first propose innovative evaluation metrics to measure search effectiveness. The findings are that (1) the Precision of expanded sets is consistently lower than that of representatives, with a decrease up to 7% at top ranks; and (2) Recall is uninformative because, for most queries, expanded sets return more records than does search of the original unclustered databases. Motivated by these findings, we propose a solution that returns a user-specified proportion of top similar records, modeled by a ranking function that aggregates sequence and annotation similarities. In experiments undertaken on UniProtKB/Swiss-Prot, the largest expert-curated protein database, we show that our method dramatically reduces the number of returned sequences, increases Precision by 3%, and does not impact effective search time.