Searching on the Secondary Structure of Protein Sequences

Summary: Proposes a query language for protein secondary structure and algorithms to evaluate queries. Implemented in Periscope and a commercial ORDBMS, with a cost-estimation based optimization framework and experiments showing protein-query performance. (summarized by gpt-5-nano on Feb 09 2026)

Paper ID: 9072
Venue: VLDB
Year: 2002
Pagerank: 5.093636e-05
Overall Rank: 12,841 | 11.90%
DOI: 10.1016/B978-155860869-6/50062-7

Incoming Non-self Citations Over Time

No non-self incoming citations found for this paper in this database.

Authors

1. Laurie Hammel (University of Michigan)
2. Jignesh M. Patel (University of Michigan)

BibTeX Citation

@article{hammel_vldb02,
        title = {{Searching on the Secondary Structure of Protein Sequences}},
        author = {Hammel, Laurie and Patel, Jignesh M.},
        journal = {PVLDB},
        series = {{VLDB} '02},
        doi = {10.1016/B978-155860869-6/50062-7},
        url = {https://doi.org/10.1016/B978-155860869-6/50062-7},
        year = {2002}
}

Incoming Citations (Sorted by Pagerank)

Showing 2 of 2 citing papers.

Rank	Citing Paper	Year	Venue	Pagerank
9,973	Exploiting Structure in Regular Expression Queries	2023	SIGMOD	5.1845938e-05
10,396	Regular Expression Indexing for Log Analysis	2026	SIGMOD	5.093636e-05

Outgoing Citations (Sorted by Pagerank)

Showing 11 of 11 cited papers.

Citations counted here include only citations to other VLDB/SIGMOD/CIDR/PODS papers in this database.

Rank	Cited Paper	Year	Venue	Pagerank
1	Access Path Selection in a Relational Database Management System	1979	SIGMOD	0.0024089429
5	Optimal Aggregation Algorithms for Middleware [Extended Abstract]	2001	PODS	0.0010828372
118	Equi-Depth Histograms For Estimating Selectivity Factors For Multi-Dimensional Queries	1988	SIGMOD	0.00031922279
170	Combining Fuzzy Information from Multiple Systems	1996	PODS	0.00027376361
274	Balancing Histogram Optimality and Practicality for Query Result Size Estimation	1995	SIGMOD	0.00022645621
299	Shoring Up Persistent Applications	1994	SIGMOD	0.00022084669
499	Supporting Incremental Join Queries on Ranked Inputs	2001	VLDB	0.00017431827
786	Universality of Serial Histograms	1993	VLDB	0.00014053885
2,008	A Database Index to Large Biological Sequences	2001	VLDB	9.310515e-05
3,207	Multi-Dimensional Substring Selectivity Estimation	1999	VLDB	7.6364508e-05
4,776	An Efficient Index Structure for String Databases	2001	VLDB	6.513844e-05

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#	Overall Rank	Paper	Year	Venue
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2	687	Sequence Query Processing	1994	SIGMOD
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4	7,823	Periscope/GQ: A Graph Querying Toolkit	2008	VLDB
5	14,116	A Database Platform for Bioinformatics	2000	VLDB
6	2,524	Optimization of Sequence Queries in Database Systems	2001	PODS
7	6,496	Reference-Based Indexing of Sequence Databases	2006	VLDB
8	591	Substructure Similarity Search in Graph Databases	2005	SIGMOD
9	2,143	An Approximate Search Engine for Structural Databases	2000	SIGMOD
10	6,229	Periscope/SQ: Interactive Exploration of Biological Sequence Databases	2007	VLDB