Parallel Solutions to the k-difference Primer Problem

  title={Parallel Solutions to the k-difference Primer Problem},
  author={Leandro Feuser and Nahri Moreano},
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… 
The main objective of this work is to minimize the execution time required for DNA global alignment of large biological sequences by dealing with the issues with the memory optimizations and minimization of execution time.
Parallelization of Global Sequence Alignment on Graphics Processing Unit
The main objective of this work is to minimize the execution time required for DNA global alignment of large biological sequences and the proposed approach covers both the memory optimizations and minimization of execution time.
Specific Substring Problem: an application in bioinformatics
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Development of a framework for whole-cell models creation
A framework with the purpose to guide and help scientists through the process of creating whole-cell models faster, enabling them to use these tools as part of their research.


Parallel Algorithms for Approximate String Matching with k Mismatches on CUDA
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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
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.
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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
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
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A polynomial-time algorithm for computing characteristic strings under a set of strings
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
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Bioinformatics Algorithms: Techniques and Applications
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Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology
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