OASIS: An Online and Accurate Technique for Local-alignment Searches on Biological Sequences
Summary: OASIS uses an A*-search over a suffix-tree index to deliver accurate Smith–Waterman local alignments on large biological datasets. For short queries it is an order of magnitude faster than SW, comparable to BLAST, and returns results in decreasing score for online use. (summarized by gpt-5-nano on Feb 09 2026)
Incoming Non-self Citations Over Time
Authors
- 1. Colin Meek
- 2. Jignesh M. Patel
- 3. Shruti Kasetty
Incoming Citations (Sorted by Pagerank)
Showing 9 of 9 citing papers.
| Rank | Citing Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 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 |
| 5,812 | Reference-Based Alignment in Large Sequence Databases | 2009 | VLDB | 5.3172025e-05 |
| 6,074 | Pigeonring: A Principle for Faster Thresholded Similarity Search | 2019 | VLDB | 5.2242306e-05 |
| 6,464 | Reference-Based Indexing of Sequence Databases | 2006 | VLDB | 5.0532607e-05 |
| 6,671 | Discovering Longest-lasting Correlation in Sequence Databases | 2013 | VLDB | 4.9669225e-05 |
| 8,706 | ALAE: Accelerating Local Alignment with Affine Gap Exactly in Biosequence Databases | 2012 | VLDB | 4.4642586e-05 |
| 9,826 | Exploiting Structure in Regular Expression Queries | 2023 | SIGMOD | 4.2751057e-05 |
| 10,106 | Regular Expression Indexing for Log Analysis | 2026 | SIGMOD | 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 |
|---|---|---|---|---|
| 415 | A Fast Index for Semistructured Data | 2001 | VLDB | 0.00023814619 |
| 1,118 | A Database Index to Large Biological Sequences | 2001 | VLDB | 0.00013879121 |
| 4,333 | An Efficient Index Structure for String Databases | 2001 | VLDB | 6.2805237e-05 |
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Semantically Similar Papers
| Overall Rank | Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 9,933 | Efficient and Effective KNN Sequence Search with Approximate n-grams | 2014 | VLDB | 4.2500258e-05 |
| 7,708 | Efficient Top-k Algorithms for Approximate Substring Matching | 2013 | SIGMOD | 4.6721808e-05 |
| 1,316 | An Approximate Search Engine for Structural Databases | 2000 | SIGMOD | 0.00012629219 |
| 12,365 | Improving Suffix Array Locality for Fast Pattern Matching on Disk | 2008 | SIGMOD | 4.1945683e-05 |
| 12,648 | Searching on the Secondary Structure of Protein Sequences | 2002 | VLDB | 4.1945683e-05 |
| 6,464 | Reference-Based Indexing of Sequence Databases | 2006 | VLDB | 5.0532607e-05 |
| 11,985 | Online Ordering of Overlapping Data Sources | 2014 | VLDB | 4.1945683e-05 |
| 5,812 | Reference-Based Alignment in Large Sequence Databases | 2009 | VLDB | 5.3172025e-05 |
| 6,107 | Continuously Adaptive Similarity Search | 2020 | SIGMOD | 5.2066612e-05 |
| 8,706 | ALAE: Accelerating Local Alignment with Affine Gap Exactly in Biosequence Databases | 2012 | VLDB | 4.4642586e-05 |