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    Seqdev: an algorithm for constructing genetic elements using comparative assembly

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    Date
    2016
    Publisher
    © 2016 Bangladesh Association for Plant Tissue
    Author
    Rahman, Tasnim
    Heickal, Hasnain
    Tabrejee, Shamira
    Chowdhury, Md Miraj Kobad
    Sarwar, Sheikh Muhammad
    Shoyaib, Mohammad
    Metadata
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    URI
    http://hdl.handle.net/10361/8092
    Citation
    Rahman, T., Heickal, H., Tabrejee, S., Chowdhury, M. M. K., Sarwar, S. M., & Shoyaib, M. (2016). Seqdev: An algorithm for constructing genetic elements using comparative assembly. Plant Tissue Culture and Biotechnology, 26(1), 105-121. doi:10.3329/ptcb.v26i1.29772
    Abstract
    With the availability of recent next generation sequencing technologies and their low cost, genomes of different organisms are being sequenced frequently. Therefore, quick assembly of genome, transcriptome, and target contigs from the raw data generated through the sequencing technologies has become necessary for better understanding of different biological systems. This article proposes an algorithm, namely SeqDev (Sequence Developer) for constructing contigs from raw reads using reference sequences. For this, we considered a weighted frequency‐based consensus mechanism named BlastAssemb for primary construction of a sequence with gaps. Then, we adopted suffix array and proposed a gap filling search (GFS) algorithm for searching the missing sequences in the primary construct. For evaluating our algorithm, we have chosen Pokkali (rice) raw genome and Japonica (rice) as our reference data. Experimental results demonstrated that our proposed algorithm accurately constructs promoter sequences of Pokkali from its raw genome data. These constructed promoter sequences were 93 ‐ 100% identical with the reference and also aligned with 96 ‐ 100% of corresponding reference sequences with eValue ranging from 0.0 ‐ 2e-14. All these results indicated that our proposed method could be a potential algorithm to construct target contigs from raw sequences with the help of reference sequences. Further wet lab validation with specific Pokkali promoter sequence will boost this method as a robust algorithm for target contig assembly.
    Keywords
    Genome sequences; Assembler; Genetic elements; Bioinformatics
     
    Description
    This article was published in Plant Tissue Culture and Biotechnology [© 2016, Bangladesh Association for Plant Tissue] and the definite version is available at: http://dx.doi.org/10.3329/ptcb.v26i1.29772. The Journal's website is at: http://www.banglajol.info/index.php/PTCB/article/view/29772
    Publisher Link
    http://www.banglajol.info/index.php/PTCB/article/view/29772
    DOI
    http://dx.doi.org/10.3329/ptcb.v26i1.29772
    Department
    Department of Mathematics and Natural Sciences, BRAC University
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