Data to form periodic lossless ternary seeds of maximum weight (Part 2)
DOI10.5281/zenodo.8395813Zenodo8395813MaRDI QIDQ6710262
Dataset published at Zenodo repository.
Author name not available (Why is that?)
Publication date: 27 September 2023
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Data to form periodic lossless ternary seeds of maximum weight. Detailed information can be found in the GitHub project (https://github.com/vtman/perlotSeeds). Codesto generate periodic blocks (binary and ternary) can also be found there. Binary seeds can have only two symbols (0 = do not care = _ or 1 = match = #). The length ofa seedis the number of its elements, weight of a seed is the number of its 1-elements. The goal is to find seeds of maximum weight, so they can be used when there are two strings with a given number of mismatches. It is observed that in many cases, these seeds of maximum weight have a periodic structure: the same block is repeated multiple times + its remainder. Blocks for binary seeds can be found with the help of the PerFSeeB project (https://github.com/vtman/PerFSeeB). These blocks have the maximum possible weight. In genetics, we have four symbols in sequences (A, C, G, T). However, the chance of having a pointwise mutation is not the same. for any pairs. Atransitionmutation (AGorCT) is often twice higher than atransversionmutation (AC,AT,GC,GT). Transition-constrained seeds use ternary alphabet {#,@,_} where@is for a match or a transition mismatch. To generate ternary seeds, we first need to generate ternary blocks. These ternary blocks can be found when we use binary blocks. However, we sometimesneed to use binary blocks for less than the maximum weight. T4V2.zip and T7V2.zip are in this dataset.
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