Genome-scale Disk-based Suffix Tree Indexing
Summary: Genome-scale disk-based suffix tree: Trellis preserves suffix links and enables external indexing for DNA sequences. Index the human genome in ~4h with 2GB RAM and ~2h suffix-link recovery, outpacing prior methods on index and query performance. (summarized by gpt-5-nano on Feb 09 2026)
Incoming Non-self Citations Over Time
Authors
- 1. Benjarath Phoophakdee (Rensselaer Polytechnic Institute)
- 2. Mohammed J. Zaki (Rensselaer Polytechnic Institute)
BibTeX Citation
@inproceedings{phoophakdee_sigmod07,
title = {{Genome-scale Disk-based Suffix Tree Indexing}},
author = {Phoophakdee, Benjarath and Zaki, Mohammed J.},
series = {{SIGMOD} '07},
booktitle = {Proceedings of the {ACM} {SIGMOD} International Conference on Management of Data},
publisher = {Association for Computing Machinery},
doi = {10.1145/1247480.1247572},
url = {https://dl.acm.org/doi/10.1145/1247480.1247572},
year = {2007}
}Incoming Citations (Sorted by Pagerank)
Showing 4 of 4 citing papers.
| Rank | Citing Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 5,364 | Serial and Parallel Methods for I/O Efficient Suffix Tree Construction | 2009 | SIGMOD | 6.1608023e-05 |
| 7,191 | ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings | 2012 | VLDB | 5.5903532e-05 |
| 12,588 | RACE: A Scalable and Elastic Parallel System for Discovering Repeats in Very Long Sequences | 2013 | VLDB | 4.9793485e-05 |
| 12,848 | Improving Suffix Array Locality for Fast Pattern Matching on Disk | 2008 | SIGMOD | 4.9793485e-05 |
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Outgoing Citations (Sorted by Pagerank)
Showing 2 of 2 cited papers.
Citations counted here include only citations to other VLDB/SIGMOD/CIDR/PODS papers in this database.
| Rank | Cited Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 2,059 | A Database Index to Large Biological Sequences | 2001 | VLDB | 9.1020248e-05 |
| 3,535 | Practical Suffix Tree Construction | 2004 | VLDB | 7.2241971e-05 |
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