ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings
Summary: ERa enables disk-based suffix-tree construction for strings larger than memory via horizontal/vertical partitioning with adaptive I/O. Serial and parallel ERa variants index the human genome in 19 minutes on a desktop; the fastest prior method runs in 15 minutes on 1024 CPUs. (summarized by gpt-5-nano on Feb 09 2026)
Incoming Non-self Citations Over Time
Authors
- 1. Essam Mansour
- 2. Amin Allam
- 3. Spiros Skiadopoulos
- 4. Panos Kalnis
Incoming Citations (Sorted by Pagerank)
Showing 2 of 2 citing papers.
| Rank | Citing Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 5,404 | Practical Authenticated Pattern Matching with Optimal Proof Size | 2015 | VLDB | 5.5267144e-05 |
| 12,100 | RACE: A Scalable and Elastic Parallel System for Discovering Repeats in Very Long Sequences | 2013 | VLDB | 4.1945683e-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 |
|---|---|---|---|---|
| 2,250 | Genome-scale Disk-based Suffix Tree Indexing | 2007 | SIGMOD | 9.2009942e-05 |
| 2,583 | Practical Suffix Tree Construction | 2004 | VLDB | 8.497732e-05 |
| 4,550 | Serial and Parallel Methods for I/O Efficient Suffix Tree Construction | 2009 | SIGMOD | 6.0924864e-05 |
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| Overall Rank | Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
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| 6,464 | Reference-Based Indexing of Sequence Databases | 2006 | VLDB | 5.0532607e-05 |
| 12,100 | RACE: A Scalable and Elastic Parallel System for Discovering Repeats in Very Long Sequences | 2013 | VLDB | 4.1945683e-05 |
| 13,455 | Memory Efficient Minimum Substring Partitioning | 2013 | VLDB | - |
| 4,333 | An Efficient Index Structure for String Databases | 2001 | VLDB | 6.2805237e-05 |
| 1,118 | A Database Index to Large Biological Sequences | 2001 | VLDB | 0.00013879121 |
| 12,365 | Improving Suffix Array Locality for Fast Pattern Matching on Disk | 2008 | SIGMOD | 4.1945683e-05 |
| 2,583 | Practical Suffix Tree Construction | 2004 | VLDB | 8.497732e-05 |
| 2,250 | Genome-scale Disk-based Suffix Tree Indexing | 2007 | SIGMOD | 9.2009942e-05 |
| 4,550 | Serial and Parallel Methods for I/O Efficient Suffix Tree Construction | 2009 | SIGMOD | 6.0924864e-05 |