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 |
|---|---|---|---|---|
| 3,138 | Genome-scale Disk-based Suffix Tree Indexing | 2007 | SIGMOD | 7.606774e-05 |
| 3,228 | OASIS: An Online and Accurate Technique for Local-alignment Searches on Biological Sequences | 2003 | VLDB | 7.5077929e-05 |
| 3,535 | Practical Suffix Tree Construction | 2004 | VLDB | 7.2241971e-05 |
| 5,364 | Serial and Parallel Methods for I/O Efficient Suffix Tree Construction | 2009 | SIGMOD | 6.1608023e-05 |
| 6,619 | Reference-Based Indexing of Sequence Databases | 2006 | VLDB | 5.7319339e-05 |
| 13,131 | Searching on the Secondary Structure of Protein Sequences | 2002 | VLDB | 4.9793485e-05 |
Previous
Page 1 / 1
Next
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 |
|---|---|---|---|---|
| 2,706 | On Effective Multi-Dimensional Indexing for Strings | 2000 | SIGMOD | 8.1111109e-05 |
Previous
Page 1 / 1
Next
Semantically Similar Papers
| # | Overall Rank | Paper | Year | Venue |
|---|---|---|---|---|
| 1 | 7,710 | The next 50 Years in Database Indexing or: The Case for Automatically Generated Index Structures | 2022 | VLDB |
| 2 | 4,734 | Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO) | 2021 | SIGMOD |
| 3 | 13,788 | On the String Matching with k Differences in DNA Databases | 2021 | VLDB |
| 4 | 6,619 | Reference-Based Indexing of Sequence Databases | 2006 | VLDB |
| 5 | 4,889 | An Efficient Index Structure for String Databases | 2001 | VLDB |
| 6 | 12,848 | Improving Suffix Array Locality for Fast Pattern Matching on Disk | 2008 | SIGMOD |
| 7 | 7,191 | ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings | 2012 | VLDB |
| 8 | 3,535 | Practical Suffix Tree Construction | 2004 | VLDB |
| 9 | 5,364 | Serial and Parallel Methods for I/O Efficient Suffix Tree Construction | 2009 | SIGMOD |
| 10 | 3,138 | Genome-scale Disk-based Suffix Tree Indexing | 2007 | SIGMOD |