This thesis describes the development and application of the new software MAXCOVER that computes maximal covers and non-extendible repeats (a.k.a. “maximal repeats”).
A string is a finite array x[1..n] of elements chosen from a set of totally ordered symbols called an alphabet. A repeat is a substring that occurs at least twice in x. A repeat is left/right extendible if every occurrence is preceded/followed by the same symbol; otherwise, it is non-left/non-right extendible (NLE/NRE). A non-extendible (NE) repeat is both NLE and NRE. A repeat covers a position i if x[i] lies within the repeat. A maximal cover (a.k.a. “optimal cover”) is a repeat that covers the most positions in x.
For simplicity, we first describe a quadratic O(n2) implementation of MAXCOVER to compute all maximal covers of a given string based on the pseudocode given in [1]. Then, we consider the logarithmic O(n log n) pseudocode in [1], in which we identify several errors. We leave a complete correction and implementation for future work. Instead, we propose two improved quadratic algorithms that, shown through experiments, will execute in linear time for the average case.
We perform a benchmark evaluation of MAXCOVER’s performance and demonstrate its value to biologists in the protein context [2]. To do so, we develop an extension of MAXCOVER for the closely related task of computing NE repeats. Then, we compare MAXCOVER to the repeat-match feature of the well-known MUMmer software [3] (600+ citations). We determine that MAXCOVER is an order-of-magnitude faster than MUMmer with much lower space requirements. We also show that MAXCOVER produces a more compact, exact, and user-friendly output that specifies the repeats.
Availability: Open source code, binaries, and test data are available on Github at https://github.com/hollykoponen/MAXCOVER. Currently runs on Linux, untested on other OS. / Thesis / Master of Science (MSc) / This thesis deals with a simple yet essential data structure called a string, a sequence of symbols drawn from an alphabet. For example, a DNA sequence is a string comprised of four letters.
We describe a new software called MAXCOVER that identifies maximal covers of a given string x (a repeating substring that ‘covers’ the most positions in x). This software is based on the algorithms in [1]. We propose two new algorithms that perform faster in practice.
We also extended MAXCOVER for the closely related task of computing non-extendible repeats. We compare this extension to the well-known MUMmer software (600+ citations). We find that MAXCOVER is many times faster than MUMmer with much lower space requirements and produces a more compact, exact and user-friendly output.
| Identifer | oai:union.ndltd.org:mcmaster.ca/oai:macsphere.mcmaster.ca:11375/27555 |
| Date | January 2022 |
| Creators | Koponen, Holly |
| Contributors | Smyth, William F., Mhaskar, Neerja, Computing and Software |
| Source Sets | McMaster University |
| Language | English |
| Detected Language | English |
| Type | Thesis |
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