Open AccessModel checking games and a genome sequence search
Author(s) -
Sergey Staroletov
Publication year - 2020
Publication title -
journal of physics. conference series
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.21
H-Index - 85
eISSN - 1742-6596
pISSN - 1742-6588
DOI - 10.1088/1742-6596/1679/3/032020
Subject(s) - computer science , model checking , encode , substring , theoretical computer science , sequence (biology) , construct (python library) , hash function , operator (biology) , algorithm , programming language , data structure , biochemistry , chemistry , genetics , repressor , biology , transcription factor , gene
The paper is considered a concept of model checking games to solve algorithmic puzzles. We describe current approaches in this field and move to a game between a user and a software model checker with the goal to provide a solution to a problem, encoded in a transition system and an LTL formula with a requirement. We show how to encode and solve some problems using this approach. Then we move to the problem of searching a pattern in a genome sequence. We implement the Z-function search method in Promela, construct the model, provide the input of real viral data, and then play a model checking game with SPIN verifier. We created a fuzzy substring search method using the non-deterministic choice operator. Based on experiments we made, we discuss that the problem to find a pattern with some deviations is only solvable using the swarm verification and hash compact methods.