Parallel Solutions to the k-difference Primer Problem

@inproceedings{Feuser2018ParallelST,
  title={Parallel Solutions to the k-difference Primer Problem},
  author={Leandro Feuser and Nahri Moreano},
  booktitle={ICCS},
  year={2018}
}
This paper presents parallel solutions to the k-difference primer problem, targeting multicore processors and GPUs. This problem consists of finding the shortest substrings of one sequence with at least k differences from another sequence. The sequences found in the solution are candidate regions to contain primers used by biologists to amplify a DNA sequence in laboratory. To the authors’ knowledge, these are the first parallel solutions proposed for the k-difference primer problem. We… 
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References

SHOWING 1-10 OF 12 REFERENCES
Parallel Algorithms for Approximate String Matching with k Mismatches on CUDA
TLDR
A new parallel programming model based on CUDA is presented and the best parallel algorithm on GPU achieves speedup of 40-80 and the OPT-block-thread parallel algorithm can take full advantage of the powerful parallel capability of GPU.
GPU accelerated inexact matching for multiple patterns in DNA sequences
  • Priyanka Rastogi, R. R. Guddeti
  • Computer Science
    2014 International Conference on Advances in Computing, Communications and Informatics (ICACCI)
  • 2014
TLDR
A parallel implementation of multiple pattern inexact matching in genome reference using CUDA based on BWT using GPGPU and incorporates DFS (Depth First Search) Strategy for matching multiple patterns.
Introducing efficient parallelism into approximate string matching and a new serial algorithm
TLDR
Given a text of length n, a pattern of length m and an integer k, this paper presents parallel and serial algorithms for finding all occurrences of the pattern in the text with at most k differences.
Fast Parallel and Serial Approximate String Matching
Efficient Implementations of the Approximate String Matching on the Memory Machine Models
  • K. Nakano
  • Computer Science
    2012 Third International Conference on Networking and Computing
  • 2012
TLDR
This paper shows efficient implementations of approximate string matching on the memory machine models DMM and UMM for strings X and Y with length m and n, respectively.
A GPGPU Implementation of Approximate String Matching with Regular Expression Operators and Comparison with Its FPGA Implementation
TLDR
An efficient GPGPU implementation of an algorithm for approximate string matching with regular expression operators, originally implemented on an FPGA, is proposed and experimental results showed that the GPU implementation is more than 18 times as fast as the CPU one when the pattern length is greater than 3200, while the FPG a one could not handle such a long pattern.
A polynomial-time algorithm for computing characteristic strings under a set of strings
TLDR
It can be decided in O(l 2 . S) time whether or not there exists a δ-characteristic string of T under S, where I is the length of a shortest string in T, and S is the size of S.
Bioinformatics - a practical guide to the analysis of genes and proteins
TLDR
This work focuses on the development of novel approaches to biological analysis using Perl to Facilitate Biological Analysis and its applications in proteomics and Protein Identification.
Bioinformatics Algorithms: Techniques and Applications
TLDR
This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology, and algorithmic approaches in structural and systems biology.
Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology
Algorithms on strings trees and sequences puter. suffix tree. algorithms on strings trees and sequences puter. algorithms on strings trees and sequences puter. algorithms on strings trees and
...
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