Feb 18, 2013 · if you have an algorithm that maps general graphs to strings, and so that two graphs map to the same string if and only if they are topologically equivalent, then you have an algorithm for GRAPH AUTOMORPHISM.

Jun 1, 2010 · Here, we show how to use suffix array-based methods that have formed the basis of recent very fast sequence mapping algorithms to find overlaps and generate assembly string graphs asymptotically faster than previously described algorithms.

Mar 25, 2025 · It is about designing algorithms that are not only correct but also optimal, taking into account factors like time and space efficiency. Algorithm design is the process of developing a step-by-step procedure to solve a specific problem. Various techniques can be used for designing algorithms, including:

Mar 11, 2022 · The Boyer-Moore algorithm is a string search algorithm that is used to find a substring in a larger string. The algorithm works by trying all possible matches for the substring and then checking whether each match is a prefix of the larger string. If the match is not a prefix, then the algorithm moves on to the next possible match.

This version of SGA also includes a faster algorithm for the core task of computing the string graph, called FSG, designed by Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, and Raffaella Rizzi.

Jul 18, 2019 · The basic data structure that you need is a node containing vertices and neighbours. So you have the word (a std::string) as vertex and the "neighbours". That is a std::vector of index positions to other nodes in the graph. The graph is a vector of nodes. And nodes neighbours point to other nodes in this vector.

Jun 12, 2021 · you can map every node to an integer with help of map<string, int>, assign every node to a different integer value, then make a graph with whose int values and run Dijkstra. For query get int value for nodes from the map and use those int values for querying.

for constructing a string graph hinders its usability for genome assembly. Even though different. NGS technologies. Therefore, in this thesis, we provide a novel, linear time and alphabet-size- efficiently construct string graph from an overlap graph. Experimental results show that …

Oct 20, 2020 · Our distributed memory algorithms for both overlap detection and layout simplification are based on linear-algebra operations over semirings using 2D distributed sparse matrices. Our layout step consists of performing a transitive reduction from the …

This repository contains implementations of classic algorithms for graphs and string matching in Java. The algorithms cover a wide range of applications, from graph processing to efficient string matching. Depth-First Search (DFS): An algorithm for traversing or searching in a graph or tree.