Seqdev: an algorithm for constructing genetic elements using comparative assembly
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
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© 2016 Bangladesh Association for Plant Tissue
2017
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| オンライン･アクセス: | http://hdl.handle.net/10361/8092 http://dx.doi.org/10.3329/ptcb.v26i1.29772 |
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10361-80922017-05-03T10:36:00Z Seqdev: an algorithm for constructing genetic elements using comparative assembly Rahman, Tasnim Heickal, Hasnain Tabrejee, Shamira Chowdhury, Md Miraj Kobad Sarwar, Sheikh Muhammad Shoyaib, Mohammad Department of Mathematics and Natural Sciences, BRAC University Genome sequences Assembler Genetic elements Bioinformatics 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 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. Published 2017-05-03T10:33:50Z 2017-05-03T10:33:50Z 2016 Article 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 18173721 http://hdl.handle.net/10361/8092 http://dx.doi.org/10.3329/ptcb.v26i1.29772 en http://www.banglajol.info/index.php/PTCB/article/view/29772 © 2016 Bangladesh Association for Plant Tissue |
| institution |
Brac University |
| collection |
Institutional Repository |
| language |
English |
| topic |
Genome sequences Assembler Genetic elements Bioinformatics |
| spellingShingle |
Genome sequences Assembler Genetic elements Bioinformatics Rahman, Tasnim Heickal, Hasnain Tabrejee, Shamira Chowdhury, Md Miraj Kobad Sarwar, Sheikh Muhammad Shoyaib, Mohammad Seqdev: an algorithm for constructing genetic elements using comparative assembly |
| 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 |
| author2 |
Department of Mathematics and Natural Sciences, BRAC University |
| author_facet |
Department of Mathematics and Natural Sciences, BRAC University Rahman, Tasnim Heickal, Hasnain Tabrejee, Shamira Chowdhury, Md Miraj Kobad Sarwar, Sheikh Muhammad Shoyaib, Mohammad |
| format |
Article |
| author |
Rahman, Tasnim Heickal, Hasnain Tabrejee, Shamira Chowdhury, Md Miraj Kobad Sarwar, Sheikh Muhammad Shoyaib, Mohammad |
| author_sort |
Rahman, Tasnim |
| title |
Seqdev: an algorithm for constructing genetic elements using comparative assembly |
| title_short |
Seqdev: an algorithm for constructing genetic elements using comparative assembly |
| title_full |
Seqdev: an algorithm for constructing genetic elements using comparative assembly |
| title_fullStr |
Seqdev: an algorithm for constructing genetic elements using comparative assembly |
| title_full_unstemmed |
Seqdev: an algorithm for constructing genetic elements using comparative assembly |
| title_sort |
seqdev: an algorithm for constructing genetic elements using comparative assembly |
| publisher |
© 2016 Bangladesh Association for Plant Tissue |
| publishDate |
2017 |
| url |
http://hdl.handle.net/10361/8092 http://dx.doi.org/10.3329/ptcb.v26i1.29772 |
| work_keys_str_mv |
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1814309096667480064 |