A Database Index to Large Biological Sequences
Summary: Adapts suffix-tree indexing to disk with PJama, enabling on-disk construction for chromosome-scale DNA sequences. Describes a tree-building algorithm, performance analysis, and interplay with object-store architectures, with early measurements. (summarized by gpt-5-nano on Feb 09 2026)
Incoming Non-self Citations Over Time
Authors
- 1. Ela Hunt (University of Glasgow)
- 2. Malcolm P. Atkinson (University of Glasgow)
- 3. Robert W. Irving (University of Glasgow)
BibTeX Citation
@article{hunt_vldb01,
title = {{A Database Index to Large Biological Sequences}},
author = {Hunt, Ela and Atkinson, Malcolm P. and Irving, Robert W.},
journal = {PVLDB},
series = {{VLDB} '01},
year = {2001}
}Incoming Citations (Sorted by Pagerank)
Showing 6 of 6 citing papers.
| Rank | Citing Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 3,077 | Genome-scale Disk-based Suffix Tree Indexing | 2007 | SIGMOD | 7.7810685e-05 |
| 3,164 | OASIS: An Online and Accurate Technique for Local-alignment Searches on Biological Sequences | 2003 | VLDB | 7.6778551e-05 |
| 3,470 | Practical Suffix Tree Construction | 2004 | VLDB | 7.3893019e-05 |
| 5,242 | Serial and Parallel Methods for I/O Efficient Suffix Tree Construction | 2009 | SIGMOD | 6.3019356e-05 |
| 6,496 | Reference-Based Indexing of Sequence Databases | 2006 | VLDB | 5.8632988e-05 |
| 12,841 | Searching on the Secondary Structure of Protein Sequences | 2002 | VLDB | 5.093636e-05 |
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Outgoing Citations (Sorted by Pagerank)
Showing 1 of 1 cited papers.
Citations counted here include only citations to other VLDB/SIGMOD/CIDR/PODS papers in this database.
| Rank | Cited Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 2,648 | On Effective Multi-Dimensional Indexing for Strings | 2000 | SIGMOD | 8.2957097e-05 |
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