The Role of The Prefix Array in Sequence Analysis: A Survey
Bibliographic record
Abstract
The prefix array was apparently first computed and used algorithmically in 1984, playing a pivotal role in an optimal algorithm to determine all the tandem repeats in a given (DNA or protein) sequence. However, it is especially since the turn of the 21st century that applications of the prefix array to fundamental sequencing problems have been recognized. An important aspect of this expanding role has been the recognition that the prefix table and the border array are “equivalent” data structures 一 that is, one can be computed from the other in linear time. Since the border array in turn specifies all the periods of every prefix of the sequence, the prefix array thus turns out to be a structure of central importance. In this paper we survey important applications of the prefix array 一 in particular to approximate string matching under Hamming distance, as well as to the computation of covers and enhanced covers 一 and show how, unlike border array algorithms, these are extendible to sequences containing “don’t-care” or indeterminate letters such as {a, c} or {g, t}. This extension leads to a surprising correspondence between prefix arrays and undirected graphs that seems likely to be a fertile source of new insights in future. We conclude with an overview of sequencing problems that the authors believe can be handled using prefix array technology.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.008 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.005 | 0.011 |
| Science and technology studies | 0.001 | 0.003 |
| Scholarly communication | 0.004 | 0.009 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.002 | 0.003 |
| Insufficient payload (model declined to judge) | 0.003 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".