@article{MAKHILLAJIT201615236624,
    title = {Improved Exact Parallel Algorithm for Planted (l, d) Motif Search},
    journal = {Asian Journal of Information Technology},
    volume = {15},
    number = {23},
    pages = {4835-4843},
    year = {2016},
    issn = {1682-3915},
    doi = {ajit.2016.4835.4843},
    url = {https://makhillpublications.co/view-article.php?issn=1682-3915&doi=ajit.2016.4835.4843},
    author = {Satarupa and},
    keywords = {Planted motif search,Symmetric Multi Processor (SMP),Message Passing Interface (MPI),bit map vector,string algorithm},
    abstract = {Motif search in computational biology is a most challenging problem. This plays a crucial role in
gene finding and understanding the gene regulation relationship. In this study, a new efficient algorithm is
proposed for the (l, d) motif search problem to find all string of length l which present in each of the input string
with d mismatches. The method is based on 2 key aspects. First, a group of 3 l-mers of close proximity is
processed efficaciously to generate the common d-neighborhood and second the data structure bit vector is
used which simplifies the process of making the union and intersection of the common d-neighborhood. The
proposed approach can be considered to be a hybrid one, as it integrates the existing algorithm with the novel
ideas of common d-neighborhood generation to achieve better running time. Moreover, a parallel version of
proposed method is also presented which runs on 4 SMP cluster systems with each of 2.4 GHz Intel Pentium-IV
having 16 GB ram running under Red Hat Linux. The experimental result shows that the proposed algorithm is
linearly scalable with the number of processors.}
    }