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**1 - 4**of**4**### Super-linear indices for approximate dictionary searching

- In SISAP
, 2012

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### Modified Suffix Search Algorithm for Multiple String Matching

"... String Matching is now a prominent field in the area of Computer Science and it has many applications in the real world. A new algorithm for Suffix Search which uses chained hashing is proposed and this works well in matched case and mismatched case. A separate hash function is introduced in this pa ..."

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String Matching is now a prominent field in the area of Computer Science and it has many applications in the real world. A new algorithm for Suffix Search which uses chained hashing is proposed and this works well in matched case and mismatched case. A separate hash function is introduced in this paper. Hash functions can be declared in many ways. In this, radix hashing is used and the need of the shift table used in these algorithms can be avoided. Every pattern matching algorithm consists of mainly two phases. They are the preprocessing phase and the matching phase. Each of these phases has its own time complexity as well as space complexity. The proposed method has very low time complexity in average case.

### Data Structure for Dynamic Patterns

"... Abstract—String matching and dynamic dictionary matching are significant principles in computer science. These principles require an efficient data structure for accommodating the pattern or patterns to be searched for in a large given text. Moreover, in the dynamic dictionary matching, the structur ..."

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Abstract—String matching and dynamic dictionary matching are significant principles in computer science. These principles require an efficient data structure for accommodating the pattern or patterns to be searched for in a large given text. Moreover, in the dynamic dictionary matching, the structure is able to insert or delete the individual patterns over time. This research article introduces a new dynamic data structure named inverted lists for both principles. The inverted lists data structure, which is derived from the inverted index, is implemented by the perfect hashing idea. This structure focuses on the position of characters and provides a hashing table to store the string patterns. The new data structure is more time efficient than traditional structures. Also, this structure is faster to construct and consumes less memory than others.

### Perfect Hashing Structures for Parallel Similarity Searches

"... Abstract—Seed-based heuristics have proved to be efficient for studying similarity between genetic databases with billions of base pairs. This paper focuses on algorithms and data structures for the filtering phase in seed-based heuristics, with an emphasis on efficient parallel GPU/manycores implem ..."

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Abstract—Seed-based heuristics have proved to be efficient for studying similarity between genetic databases with billions of base pairs. This paper focuses on algorithms and data structures for the filtering phase in seed-based heuristics, with an emphasis on efficient parallel GPU/manycores implementa-tion. We propose a 2-stage index structure which is based on neighborhood indexing and perfect hashing techniques. This structure performs a filtering phase over the neighborhood regions around the seeds in constant time and avoid as much as possible random memory accesses and branch divergences. Moreover, it fits particularly well on parallel SIMD processors, because it requires intensive but homogeneous computational operations. Using this data structure, we developed a fast and sensitive OpenCL prototype read mapper. Keywords-seed-based heuristics; perfect hash function; par-allelism; GPU; OpenCL; read mapper I.