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
- 2. Malcolm P. Atkinson
- 3. Robert W. Irving
Incoming Citations (Sorted by Pagerank)
Showing 6 of 6 citing papers.
| Rank | Citing Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 2,251 | Genome-scale Disk-based Suffix Tree Indexing | 2007 | SIGMOD | 9.1921005e-05 |
| 2,500 | OASIS: An Online and Accurate Technique for Local-alignment Searches on Biological Sequences | 2003 | VLDB | 8.6388583e-05 |
| 2,586 | Practical Suffix Tree Construction | 2004 | VLDB | 8.4894627e-05 |
| 4,550 | Serial and Parallel Methods for I/O Efficient Suffix Tree Construction | 2009 | SIGMOD | 6.0866239e-05 |
| 6,458 | Reference-Based Indexing of Sequence Databases | 2006 | VLDB | 5.0484248e-05 |
| 12,657 | Searching on the Secondary Structure of Protein Sequences | 2002 | VLDB | 4.1905499e-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 |
|---|---|---|---|---|
| 1,184 | On Effective Multi-Dimensional Indexing for Strings | 2000 | SIGMOD | 0.00013442644 |
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Semantically Similar Papers
| Overall Rank | Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 8,408 | The next 50 Years in Database Indexing or: The Case for Automatically Generated Index Structures | 2022 | VLDB | 4.5159669e-05 |
| 4,375 | Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO) | 2021 | SIGMOD | 6.2345844e-05 |
| 13,285 | On the String Matching with k Differences in DNA Databases | 2021 | VLDB | - |
| 6,458 | Reference-Based Indexing of Sequence Databases | 2006 | VLDB | 5.0484248e-05 |
| 4,330 | An Efficient Index Structure for String Databases | 2001 | VLDB | 6.2745131e-05 |
| 12,373 | Improving Suffix Array Locality for Fast Pattern Matching on Disk | 2008 | SIGMOD | 4.1905499e-05 |
| 6,319 | ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings | 2012 | VLDB | 5.1083749e-05 |
| 2,586 | Practical Suffix Tree Construction | 2004 | VLDB | 8.4894627e-05 |
| 4,550 | Serial and Parallel Methods for I/O Efficient Suffix Tree Construction | 2009 | SIGMOD | 6.0866239e-05 |
| 2,251 | Genome-scale Disk-based Suffix Tree Indexing | 2007 | SIGMOD | 9.1921005e-05 |