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Abstract

Basic Local Alignment Sequencing Tool (BLAST) is a bioinformatics tool used for analyzing nucleotide sequences with regards to their similarity. BLAST can be found online on biological databases such as the National Center for Biotechnology Information (NCBI) and other such repositories. The mechanism of BLAST allows the target sequence to be compared with other sequences to find regions of local similarity, and thus, a comparability quotient that determines the resemblance between the sequences is created. Due to the open-platform nature of the online databanks, several sequences can be accepted with little to no interjections regarding the quality of sequence submitted. An example of unclean nucleotide sequences can be based on the number of non-template nucleotides, denoted as “N,” present within the sequence. Here we develop a self-established nucleotide sequence reading program known as “DNAChecker,” which helps identify the quality of the target sequence and therefore proposes the effectiveness of the BLAST result. DNAChecker is an inbuilt, program that runs on Python 3.4 and was implemented in the United States Agency for International Development (USAID) project conducted in Indonesia International Institute for Life Sciences. Although DNAChecker has proven to be useful, it has a lot of room for improvements, such as having a more objectively accurate means of differentiating between good and bad sequences.

Bahasa Abstract

Penggunaan Algoritma “DNA Checker” untuk Pengembangan Riset Bioinformatika. Basic Sequence Alignment Tool (BLAST) adalah aplikasi bioinformatika yang digunakan untuk menganalisis sekuens nukleotida sehubungan dengan pensejajarannya. BLAST dapat ditemukan secara daring di database biologis seperti Pusat Nasional untuk Informasi Bioteknologi (NCBI) dan repositori lainnya. Mekanisme BLAST memungkinkan sekuens target untuk dibandingkan dengan sekuens lain untuk menemukan daerah kesamaan lokal, dan dengan demikian, dapat menghasilkan perbandingan yang menentukan kemiripan antara sekuens. Karena sifat platform terbuka dari bank data daring, beberapa urutan dapat diterima dengan sedikit atau tanpa interupsi terkait kualitas urutan yang disampaikan. Contoh urutan nukleotida tidak baik dapat didasarkan pada jumlah nukleotida non-template, dilambangkan sebagai "N," yang hadir dalam urutan. Di sini kami mengembangkan program pembacaan urutan nukleotida yang dikenal sebagai "DNAChecker," yang membantu mengidentifikasi kualitas urutan target dan karenanya meningkatkan keefektifan hasil pencarian BLAST. DNAChecker adalah program inbuilt, yang berjalan pada Python 3.4 dan diimplementasikan di proyek Badan Pembangunan Internasional Amerika Serikat (USAID) yang dilaksanakan di Institut Bioscientia Internasional Indonesia. Meskipun DNAChecker terbukti bermanfaat, ia tetap seyogyanya ditingkatkan fiturnya, seperti memiliki cara yang lebih akurat secara obyektif untuk membedakan urutan yang baik dan buruk.

References

  1. M. Johnson, I. Zaretskaya, Y. Raytselis, Y. Merezhuk, S. McGinnis, T.L. Madden, Nucleic Acids Res. 36 (2008) W5-9.
  2. P. Rice, I. Longden, A. Bleasby, Trends Genet. 16 (2000) 276.
  3. D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, E.W. Sayers, Nucleic Acids Res. 37 (2009) D26.
  4. B. Steipe, B. Schiller, A. Plückthun, S. Steinbacher, J. Mol. Biol. 240 (1994) 188.
  5. E.H. Akand, K.M. Downard, Mol. Phylogenet. Evol. 112 (2017) 209.
  6. P.J.A. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski, M.J.L. de Hoon, Bioinformatics 25 (2009) 1422.
  7. B. Chapman, J. Chang, ACM SIGBIO Newsl. 20 (2000) 15.
  8. M.I. Khan, C. Sheel, Am. J. Bioinforma. 2 (2013) 15.
  9. D.P. M., R. Prabha, A. Rai, D.K. Arora, Am. J. Bioinforma. 1 (2012) 10.
  10. R.M. Al-Khatib, R. Abdullah, N.A. Rashid, J. Comput. Sci. 5 (2009) 680.
  11. K.N. Mishra, D.A. Aaggarwal, D.E. Abdelhadi, D.P.C. Srivastava, Int. J. Comput. Appl. 3 (2010) 39.
  12. N. Tabuchi, E. Sumii, A. Yonezawa, Electron. Notes Theor. Comput. Sci. 75 (2003) 95.
  13. J.C. Brown, J. Virol. Antivir. Res. 5 (2016) 1.
  14. B. Steele, J. Chandler, S. Reddy, in: Algorithms Data Sci., Springer International Publishing, Cham, 2016, pp. 313–342.
  15. T. Cajka, L.A. Garay, I.R. Sitepu, K.L. BoundyMills, O. Fiehn, J. Nat. Prod. 79 (2016) 2580.
  16. L.A. Garay, I.R. Sitepu, T. Cajka, O. Fiehn, E. Cathcart, R.W. Fry, A. Kanti, A. Joko Nugroho, S.A. Faulina, S. Stephanandra, J.B. German, K.L. Boundy-Mills, J. Ind. Microbiol. Biotechnol. 44 (2017) 1.
  17. L.A. Garay, I.R. Sitepu, T. Cajka, I. Chandra, S. Shi, T. Lin, J.B. German, O. Fiehn, K.L. BoundyMills, J. Ind. Microbiol. Biotechnol. 43 (2016) 887.
  18. P.J.A. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J.Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B.Wilczynski, M.J.L. de Hoon. Bioinf. 25 (2009) 1422.
  19. B. Chapman, Genome Informatics 299 (2003) 298.
  20. A.A. Parikesit, P.F. Stadler, S.J. Prohaska, Open Ser. Informatics 4 (2012) 1.
  21. A.A. Parikesit, S. Prohaska, P. Stadler, N. Biotechnol. 27 (2010) S44.
  22. A.A. Parikesit, P.F. Stadler, S.J. Prohaska, in: Ext. Abstr. Ger. Conf. Bioinforma., 2011, pp. 9–11.

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