Serial and Parallel Methods for I/O Efficient Suffix Tree Construction
Summary: Suffix-tree construction re-architected as a tiled, constant-working-set workflow for I/O-efficient scaling beyond main memory. On massively parallel platforms (Blue Gene/L), locality-aware design and efficient communication yield major speedups, indexing the human genome on 1024 CPUs in under 15 minutes. (summarized by gpt-5-nano on Feb 09 2026)
Incoming Non-self Citations Over Time
Authors
- 1. Amol Ghoting (IBM)
- 2. Konstantin Makarychev (IBM)
BibTeX Citation
@inproceedings{ghoting_sigmod09,
title = {{Serial and Parallel Methods for I/O Efficient Suffix Tree Construction}},
author = {Ghoting, Amol and Makarychev, Konstantin},
series = {{SIGMOD} '09},
booktitle = {Proceedings of the {ACM} {SIGMOD} International Conference on Management of Data},
publisher = {Association for Computing Machinery},
doi = {10.1145/1559845.1559931},
url = {https://dl.acm.org/doi/10.1145/1559845.1559931},
year = {2009}
}Incoming Citations (Sorted by Pagerank)
Showing 2 of 2 citing papers.
| Rank | Citing Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 7,057 | ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings | 2012 | VLDB | 5.7159515e-05 |
| 12,297 | RACE: A Scalable and Elastic Parallel System for Discovering Repeats in Very Long Sequences | 2013 | VLDB | 5.093636e-05 |
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Outgoing Citations (Sorted by Pagerank)
Showing 3 of 3 cited papers.
Citations counted here include only citations to other VLDB/SIGMOD/CIDR/PODS papers in this database.
| Rank | Cited Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 2,008 | A Database Index to Large Biological Sequences | 2001 | VLDB | 9.310515e-05 |
| 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 |
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