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    % 변경전 제목
    % \title{3D Graphical Representation of DNA Sequences and its Application for Long Sequence Searching over Whole Genomes}
    %\title{3D Graphical Representation of Whole Genome Sequence and its Application for Query Sequence Length Adaptive Searching }
    \title{ Alignment-free Sequence Searching over Whole Genomes \\Using 3D Random plot of Query DNA Sequences }
    \author{Da-Young Lee, Hae-Sung Tak, Han-Ho Kim, Hwan-Gue Cho \\
      Dept. of Electrical and Computer Engineering, Pusan National University, South Korea\\
      E-mail: \{schematique, tok33, quant1216, hgcho\}@pusan.ac.kr}
  \titleodd{ Alignment-free Sequence Searching over Whole Genomes\ldots}
 % \authoreven{Da-Young Lee et al.}
  \keywords{ Sequence Search, Sequence Visualization, Whole Genome, 3D Random Plot }
  \received{March 29, 2018}

  \abstract{
        %유전체 데이터 연구는 서열의 비교 및 탐색을 기반으로 이루어 진다.
        %alignment algorithm을 기반으로 한 비교 모델이 가장 보편적으로 활용된다.
        Most genomic data studies are based on sequence comparisons and searches, and comparison models based on alignment algorithms are most commonly used.
        %이 방법은 매우 정확하지만, n이 서열의 길이라고 가정 했을 때, n^2의 공간 및 시간 복잡도를 필요로 하기 때문에, kilobytes 단위의 짧은 서열을 쿼리를 사용할 때 유용하다.
        This method is very accurate, but it is useful when the query is short in kilobytes, because it requires the quadratic time and space complexity, $O(n^2)$ where $n$ is the length of target and query sequences.
        %NGS 기술의 발달로 megabyte 크기의 전유전체 데이터에 관한 연구가 활발히 이루어지는 가운데, 대용량 서열 데이터에 대한 새로운 비교 및 서열 탐색 방법이 필요하다.
        With the development of Next Generation Sequencing techniques, researches on whole genome sequence data of megabyte size are being actively studied, and new comparison and search methods for large-scale sequence data are needed.
        %따라서 본 연구에서는 alignment 기반 모델의 한계를 극복하기 위해 그래픽 기반의 alignment-free 서열 비교 및 탐색 모델을 제안하고자 한다.
        We propose a new alignment-free sequence comparison and search method to overcome the limitations of the alignment-based model.
        In this graphical model, the sequence searching problem in DNA strings can be reduced to find some parts of geometric object within a relatively small-scale geometric space.
        When comparing similarity by modifying sequences of similar length, we can confirm that the comparison model is appropriate by accurately reflecting the degree of similarity.
        When searching the query sequence comparison model based on 200MB sized whole genome sequence, using the compressed coordinate information, it was able to search the 10MB sequences in 22s, which is a very reduced time compared to alignment.
        Although it is not possible to find the exact position of the base pair unit as in the alignment result, it is a model that can be used as a preprocessing process to quickly search a whole genome sequence of several hundred megabytes-size.
%        With the development of Next Generation Sequencing techniques, the analysis of megabyte-sized whole genome sequence has been common.
%        In general genome sequence comparison is conducted by alignment algorithm model.
%        For example Needleman–Wunsch algorithm is one of typical techniques in comparing DNA sequences.
%        It is accurate, but assuming that the length of the target sequence is short(less than a few kilobytes) since it requires the quadratic time and space complexity, $O(n^2)$ where $n$ is the length of target and query sequences.
%        So the alignment algorithms has not been utilized in the megabytes whole genome scales.
%        Instead, heuristic algorithms such as BLAST are used for local and global similarity search. \par
%        To overcome these drawbacks in whole genome scale comparison, we suggest a new method for finding local similar subsequences among whole genomes based on random plot visualization.
%        So that the sequence searching problem in DNA strings can be reduced to find some parts of geometric object within a relatively small-scale geometric space.
%        When comparing similarity by modifying sequences of similar length, we can confirm that the comparison model is appropriate by accurately reflecting the degree of similarity.
%        When searching the query sequence comparison model based on 200MB sized whole genome sequence, using the compressed coordinate information, it was able to search the 10MB sequences in 22s, which is a very reduced time compared to alignment.
  }
  \abstractSi{ Na podlagi te vizualizacije celotnega zaporedja smo pokazali, da je na dolžini poizvedbe mogoče prilagodljivo hitro iskanje. }
  % 슬로베키아 언어로 요약문 쓰기
  % \abstractSi{전체 시퀀스의 시각화를 기반으로 쿼리 길이에 대해 빠른 검색이 가능하다는 것을 보여주었습니다.}
  \maketitle

    \section{Introduction}
    \input{JofInfor-introduction}
    \section{Related Work}
    \input{JofInfor-relatedWork1}
    \input{JofInfor-relatedWork2}
    \section{New method using 3D Random Plot}
    \input{JofInfor-method}
    \section{Experiments}
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    \section{Conclusion}
    \input{JofInfor-conclusion}

\subsection*{Acknowledgement}
This research was supported by the Collaborative Genome Program of the Korea Institute of Marine Science and Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries (MOF) (No. 20140428).
%This research was supported by the Collaborative Genome Program for Fostering New Post-Genome Industry of the Korea Institute of Marine Science and Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries (MOF) (No. 20140428).

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