Banner
Current IssueEditorial BoardOnline First ArticlesArchive
Current IssueEditorial BoardOnline First ArticlesArchive

Research Article

volume 36 issue 1 (march 2021) : 55-61,   Doi: 10.18805/BKAP283

Understanding the BLAST (Basic Local Alignment Search Tool) Program and a Step-by-step Guide for its use in Life Science Research

K
Kailash Chandra Samal
J
Jyoti Prakash Sahoo
L
Laxmipreeya Behera
T
Trupti Dash
1Department of Agricultural Biotechnology, Odisha University of Agriculture and Technology, Bhubaneswar-751 003, Odisha, India.

  • Submitted24-05-2021|

  • Accepted22-06-2021|

  • First Online 26-06-2021|

  • doi 10.18805/BKAP283

Cite article:- Samal Chandra Kailash, Sahoo Prakash Jyoti, Behera Laxmipreeya, Dash Trupti (2021). Understanding the BLAST (Basic Local Alignment Search Tool) Programand a Step-by-step Guide for its use in Life Science Research. Bhartiya Krishi Anusandhan Patrika. 36(1): 55-61. doi: 10.18805/BKAP283.

ABSTRACT

Bioinformatics is the new branch of science which deals with the acquisition, storage, analysis and dissemination of biological data with the help of computer science and information technology. It has the enormous ability to analyze a vast quantity of biological data quickly and cost-effectively. In the past decades, enormous sequence information has been generated due to the advances in DNA and protein sequencing techniques. Estimating similarities between biological sequences is becoming necessary to obtain hidden information present within the sequence and to trace evolutionary relationship exist within the sequences. This sequence comparison can be achieved by basic local alignment search tool (BLAST). So BLAST has become a fundamental tools of life science research. Hence it is essential to know how to do sequence comparison using BLAST and how to accurately interpret the BLAST output data. The present article aims to familiarize the biologists and researchers with different BLAST programs and their use in research program.

REFERENCES

  1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. (1990). Basic alignment search tools. J. Mol. Biol. 215: 403-410.
  2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research. 25: 3389-3402.
  3. Boratyn, G.M., Schäffer, A.A., Agarwala, R., Altschul, S.F., Lipman, D.J. and Madden, T.L. (2012). Domain enhanced lookup time accelerated BLAST. Biology direct. 7: 12. https://doi.org/10.1186/1745-6150-7-12.
  4. Dereeper, A., Audic, S., Claverie, J-M., Blanc, G. (2010). BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BioMed Central Evolutionary Biology. 10(8) pp. 1-6.
  5. Eric S. Donkor, Nicholas, T.K.D. Dayie and Theophilus K. Adiku, (2014). Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA). Journal of Bioinformatics and Sequence Analysis. 6(1): 1-6.
  6. Henikoff, S., Henikoff, J.G. (2000). Amino acid substitution matrices. Adv. Protein Chem. 54: 73-97.
  7. Holton, W.C. (2004). The Path to Species Comparison. In: Environmental Health Perspectives 112(12): A 672.
  8. https://blast.ncbi.nlm.nih.govBLAST: Basic Local Alignment Search Tool.
  9. Kelly, S., Maini, P.K. (2013). Dendro BLAST: Approximate Phylogenetic Trees in the absence of Multiple Sequence Alignments. PLOS ONE. 8(3): e58537 pp. 1-11.
  10. Lu, G., Jiang, L., Helikar, R.M.K., Rowley, T.W., Zhang, L., Chen, X., Moriyama, E.N. (2006). Genome Blast: a web tool for small genome comparison. BioMed Central Bioinformatics, 7(Suppl 4): S18: 1- 9.
  11. McGinnis, S. and Madden, T.L. (2004). BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32(Web Server issue): W20-W25.
  12. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C., Kanehisa, M. (2007). KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research. 35: W182-W185.
  13. Mount, D.W. (2004). Alignment of pairs of sequences. In Bioinformatics: Sequence and Genome Analysis, 2nd edition, by David W. Mount. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
  14. Mount DW (2008). Using gaps and gap penalties to optimize pairwise sequence alignments. CSH Protoc, 2008: pdb top40.
  15. National Institutes of Health. (2010). NIH working definition of bioinformatics and computational biology. Bethesda, USA. http://www.bisti.nih.gov/docs/CompuBioDef.pdf.
  16. Parra, G., Agarwal, P., Abril, J.F., Wiehe, T., Fickett, J.W. and Guigo, R. (2003). Comparative Gene Prediction in Human and Mouse. Genome Research. 13: 108-117.
  17. Schaffer, A.A., Aravind, L., Madden, T.L., Shavirin, S., Spouge, J.L., Wolf, Y.I., Koonin, E.V., Altschul, SF. (2001). Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 2001 29(14): 2994-3005
  18. Smith, T.F. and Waterman, M.S. (1981). Identification of common molecular subsequences. J. Mol Biol. 147(1): 195-197.
  19. Syngai, G.G., Barman, P., Bharali, R. and Dey, S. (2013). BLAST: An introductory tool for students to Bioinformatics Applications. Keanean Journal of Science. 2: 67-76.
  20. vanHijum, S.A.F.T., Zomer, A.L., Kuipers, O.P., Kok, J. (2005). Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Research 33: W560-W566.
  21. Wootton, J.C. and Federhen, S. (1993). Statistics of local complexity in amino acid sequences and sequence databases.Computers in Chemistry. 17: 149-163.
  22. Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., and Madden, T.L. (2012). Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 13:134.
  23. Ye, J., Ma, N., Madden, T.L., and Ostell, J.M. (2013). IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 2013 Jul; 41: W34-W40
  24. Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., Madden, T.L. (2012). Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BioMed Central Bioinformatics. 13(134): 1-11.
  25. Zhang, Z., Carriero, N., Zheng, D., Karro, J., Harrison, P.M., Gerstein, M. (2006). PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics. 22(12): 1437-1439. 
Published In
Bhartiya Krishi Anusandhan Patrika
Article Metrics
Metrics Icon
0
Views
0
Citations
Reviewed By
Share Article
Download Article
In this Article
    Contact us
    Follow us

    Research Article

    volume 36 issue 1 (march 2021) : 55-61,   Doi: 10.18805/BKAP283

    Understanding the BLAST (Basic Local Alignment Search Tool) Program and a Step-by-step Guide for its use in Life Science Research

    K
    Kailash Chandra Samal
    J
    Jyoti Prakash Sahoo
    L
    Laxmipreeya Behera
    T
    Trupti Dash
    1Department of Agricultural Biotechnology, Odisha University of Agriculture and Technology, Bhubaneswar-751 003, Odisha, India.

    • Submitted24-05-2021|

    • Accepted22-06-2021|

    • First Online 26-06-2021|

    • doi 10.18805/BKAP283

    Cite article:- Samal Chandra Kailash, Sahoo Prakash Jyoti, Behera Laxmipreeya, Dash Trupti (2021). Understanding the BLAST (Basic Local Alignment Search Tool) Programand a Step-by-step Guide for its use in Life Science Research. Bhartiya Krishi Anusandhan Patrika. 36(1): 55-61. doi: 10.18805/BKAP283.

    ABSTRACT

    Bioinformatics is the new branch of science which deals with the acquisition, storage, analysis and dissemination of biological data with the help of computer science and information technology. It has the enormous ability to analyze a vast quantity of biological data quickly and cost-effectively. In the past decades, enormous sequence information has been generated due to the advances in DNA and protein sequencing techniques. Estimating similarities between biological sequences is becoming necessary to obtain hidden information present within the sequence and to trace evolutionary relationship exist within the sequences. This sequence comparison can be achieved by basic local alignment search tool (BLAST). So BLAST has become a fundamental tools of life science research. Hence it is essential to know how to do sequence comparison using BLAST and how to accurately interpret the BLAST output data. The present article aims to familiarize the biologists and researchers with different BLAST programs and their use in research program.

    REFERENCES

    1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. (1990). Basic alignment search tools. J. Mol. Biol. 215: 403-410.
    2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research. 25: 3389-3402.
    3. Boratyn, G.M., Schäffer, A.A., Agarwala, R., Altschul, S.F., Lipman, D.J. and Madden, T.L. (2012). Domain enhanced lookup time accelerated BLAST. Biology direct. 7: 12. https://doi.org/10.1186/1745-6150-7-12.
    4. Dereeper, A., Audic, S., Claverie, J-M., Blanc, G. (2010). BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BioMed Central Evolutionary Biology. 10(8) pp. 1-6.
    5. Eric S. Donkor, Nicholas, T.K.D. Dayie and Theophilus K. Adiku, (2014). Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA). Journal of Bioinformatics and Sequence Analysis. 6(1): 1-6.
    6. Henikoff, S., Henikoff, J.G. (2000). Amino acid substitution matrices. Adv. Protein Chem. 54: 73-97.
    7. Holton, W.C. (2004). The Path to Species Comparison. In: Environmental Health Perspectives 112(12): A 672.
    8. https://blast.ncbi.nlm.nih.govBLAST: Basic Local Alignment Search Tool.
    9. Kelly, S., Maini, P.K. (2013). Dendro BLAST: Approximate Phylogenetic Trees in the absence of Multiple Sequence Alignments. PLOS ONE. 8(3): e58537 pp. 1-11.
    10. Lu, G., Jiang, L., Helikar, R.M.K., Rowley, T.W., Zhang, L., Chen, X., Moriyama, E.N. (2006). Genome Blast: a web tool for small genome comparison. BioMed Central Bioinformatics, 7(Suppl 4): S18: 1- 9.
    11. McGinnis, S. and Madden, T.L. (2004). BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32(Web Server issue): W20-W25.
    12. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C., Kanehisa, M. (2007). KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research. 35: W182-W185.
    13. Mount, D.W. (2004). Alignment of pairs of sequences. In Bioinformatics: Sequence and Genome Analysis, 2nd edition, by David W. Mount. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
    14. Mount DW (2008). Using gaps and gap penalties to optimize pairwise sequence alignments. CSH Protoc, 2008: pdb top40.
    15. National Institutes of Health. (2010). NIH working definition of bioinformatics and computational biology. Bethesda, USA. http://www.bisti.nih.gov/docs/CompuBioDef.pdf.
    16. Parra, G., Agarwal, P., Abril, J.F., Wiehe, T., Fickett, J.W. and Guigo, R. (2003). Comparative Gene Prediction in Human and Mouse. Genome Research. 13: 108-117.
    17. Schaffer, A.A., Aravind, L., Madden, T.L., Shavirin, S., Spouge, J.L., Wolf, Y.I., Koonin, E.V., Altschul, SF. (2001). Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 2001 29(14): 2994-3005
    18. Smith, T.F. and Waterman, M.S. (1981). Identification of common molecular subsequences. J. Mol Biol. 147(1): 195-197.
    19. Syngai, G.G., Barman, P., Bharali, R. and Dey, S. (2013). BLAST: An introductory tool for students to Bioinformatics Applications. Keanean Journal of Science. 2: 67-76.
    20. vanHijum, S.A.F.T., Zomer, A.L., Kuipers, O.P., Kok, J. (2005). Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Research 33: W560-W566.
    21. Wootton, J.C. and Federhen, S. (1993). Statistics of local complexity in amino acid sequences and sequence databases.Computers in Chemistry. 17: 149-163.
    22. Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., and Madden, T.L. (2012). Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 13:134.
    23. Ye, J., Ma, N., Madden, T.L., and Ostell, J.M. (2013). IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 2013 Jul; 41: W34-W40
    24. Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., Madden, T.L. (2012). Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BioMed Central Bioinformatics. 13(134): 1-11.
    25. Zhang, Z., Carriero, N., Zheng, D., Karro, J., Harrison, P.M., Gerstein, M. (2006). PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics. 22(12): 1437-1439. 
    In this Article
      Contact us
      Follow us
      Published In
      Bhartiya Krishi Anusandhan Patrika

      Editorial Board

      View all (0)