Published November 10, 2025
| Version v1
Book chapter
Open
Bioinformatics Basics: Tools and Techniques for Modern Biology
Authors/Creators
- 1. Department of Botany, Shri Pancham Khemaraj Mahavidyalaya (Autonomous) Sawantwadi, Sindhudurg, (MH), India.
Description
Data storage, accessibility, genomics, proteomics, and individualized treatment depend on biological databases in modern research. Researchers can easily access complex biological data from their huge biological data stores. By including biological data, public databases enable worldwide collaboration and tailored therapy to study genetic variation health effects. Nucleic acid, protein, and gene expression databases are needed due to the exponential development of biological data. In biotechnology, GenBank, DDBJ, and EMBL foster collaboration and research. Researchers utilize Entrez and BLAST to quickly retrieve and align sequences to study biological systems and pathologies. As the landscape evolves, these databases will aid information sharing and biological evolution.
Files
1. Dr. Aparadh Vishal Tukaram.pdf
Files
(416.4 kB)
| Name | Size | Download all |
|---|---|---|
|
md5:15f2db430443dcf844c03b4f21ed188a
|
416.4 kB | Preview Download |
Additional details
References
- 1. Abugessaisa, I., & Kasukawa, T. (Eds.). (2021). Practical guide to life science databases. Springer. 2. Apweiler, R. (2001). Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences. Briefings in Bioinformatics, 2(1), 9-18. 3. Arora, T., & Malik, A. A. (2021). An introduction to BLAST: applications for computer-aided drug design and development. In Chemoinformatics and bioinformatics in the pharmaceutical sciences (pp. 423-453). Academic Press. 4. Bairoch, A., Apweiler, R., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., ... & Yeh, L. S. L. (2005). The universal protein resource (UniProt). Nucleic acids research, 33(suppl_1), D154-D159. 5. Barker, W. C., Garavelli, J. S., Haft, D. H., Hunt, L. T., Marzec, C. R., Orcutt, B. C., ... & Tsugita, A. (1998). The PIR-international protein sequence database. Nucleic Acids Research, 26(1), 27-32. 6. Barker, W. C., Garavelli, J. S., McGarvey, P. B., Marzec, C. R., Orcutt, B. C., Srinivasarao, G. Y., ... & Wu, C. (1999). The PIR-international protein sequence database. Nucleic Acids Research, 27(1), 39-43. 7. Barker, W. C., George, D. G., Mewes, H. W., & Tsugita, A. (1992). The PIR-International protein sequence database. Nucleic acids research, 20(Suppl), 2023. 8. Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2012). GenBank. Nucleic acids research, 41(D1), D36-D42. 9. Benson, D. A., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2014). GenBank. Nucleic acids research, 43(Database issue), D30. 10. Bienert, S., Waterhouse, A., De Beer, T. A., Tauriello, G., Studer, G., Bordoli, L., & Schwede, T. (2017). The SWISS-MODEL Repository—new features and functionality. Nucleic acids research, 45(D1), D313-D319. 11. Birney, E. (2023). Big Data in Biology: How EMBL delivers big data for biology, and some highlights of its application to human disease biology. In 4th Belgrade Bioinformatics Conference (Vol. 4, pp. 1-1). Belgrade: Institute of molecular genetics and genetic engineering. 12. Boeckmann, B., Blatter, M. C., Famiglietti, L., Hinz, U., Lane, L., Roechert, B., & Bairoch, A. (2005). Protein variety and functional diversity: Swiss-Prot annotation in its biological context. Comptes rendus biologies, 328(10-11), 882-899. 13. Brunner, D., Durinx, C., Erb, M., Fischer, M., Hari, Y., Jazwinska, A., ... & Walter, A. (2021). Biology Roadmap: For Research Infrastructures 2025-2028 by the Swiss Biology Community. Swiss Academies Reports, 16(2). 14. Can, T. (2013). Introduction to bioinformatics. In miRNomics: MicroRNA biology and computational analysis (pp. 51-71). Totowa, NJ: Humana Press. 15. Cannataro, M., Guzzi, P. H., Tradigo, G., & Veltri, P. (2014). Biological databases. In Springer Handbook of Bio-/Neuroinformatics (pp. 431-440). Berlin, Heidelberg: Springer Berlin Heidelberg. 16. Cantelli, G., Bateman, A., Brooksbank, C., Petrov, A. I., Malik-Sheriff, R. S., Ide-Smith, M., ... & McEntyre, J. (2022). The european bioinformatics institute (EMBL-EBI) in 2021. Nucleic Acids Research, 50(D1), D11-D19. 17. Cassata, F., & de Chadarevian, S. (2025). Asilomar Across the Atlantic: EMBO, EMBL, and the Politics of Scientific Expertise. Journal of the History of Biology, 58(1), 95-132. 18. Cassata, F. (2024). A 'heavy hammer to crack a small nut'? The creation of the European Molecular Biology Conference (EMBC), 1963–1970. Annals of Science, 1-48. 19. Chen, C., Huang, H., & Wu, C. H. (2010). Protein bioinformatics databases and resources. Bioinformatics for Comparative Proteomics, 3-24. 20. Chen, J., & Coppola, G. (2018). Bioinformatics and genomic databases. Handbook of Clinical Neurology, 147, 75-92. 21. Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2016). GenBank. Nucleic acids research, 44(D1), D67-D72. 22. Diniz, W. J. D. S., & Canduri, F. (2017). Bioinformatics: an overview and its applications. Genet Mol Res, 16(1), 17. 23. Diniz, W. J. D. S., & Canduri, F. (2017). Bioinformatics: an overview and its applications. Genet Mol Res, 16(1), 17. 24. Diniz, W. J. D. S., & Canduri, F. (2017). Bioinformatics: an overview and its applications. Genet Mol Res, 16(1), 17. 25. Donkor, E. S., Dayie, N. T., & Adiku, T. K. (2014). Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA). Journal of Bioinformatics and sequence analysis, 6(1), 1-6. 26. Edwards, Y. J., & Cottage, A. (2003). Bioinformatics methods to predict protein structure and function: A practical approach. Molecular biotechnology, 23(2), 139-166. 27. Gasteiger, E., Jung, E., & Bairoch, A. (2001). SWISS-PROT: connecting biomolecular knowledge via a protein database. Current issues in molecular biology, 3(3), 47-55. 28. Gauthier, J., Vincent, A. T., Charette, S. J., & Derome, N. (2019). A brief history of bioinformatics. Briefings in bioinformatics, 20(6), 1981-1996. 29. George, D. G., & Hunt, L. T. (2012). THE PROTEIN IDENTIFICATION RESOURCE (PIR): AN ON-LINE COMPUTER SYSTEM. Proteins: Structure and Function, 445. 30. George, D. G., Barker, W. C., & Hunt, L. T. (1987). The Protein Identification Resource (PIR): An On-Line Computer System for the Characterization of Proteins Based on Comparisons with Previously Characterized Protein Sequences. In Proteins: Structure and Function (pp. 445-453). Boston, MA: Springer US. 31. George, D. G., Hunt, L. T., & Barker, W. C. (1996). [3] PIR-International protein sequence database. In Methods in enzymology (Vol. 266, pp. 41-59). Academic Press. 32. Gray, J. (2022). Brief Guide to Conducting Biological Database Searches. In Molecular Analyses (pp. 209-224). CRC Press. 33. Gromiha, M. M. (2011). Protein bioinformatics: from sequence to function. academic press. 34. Guex, N., Peitsch, M. C., & Schwede, T. (2009). Automated comparative protein structure modeling with SWISS‐MODEL and Swiss‐PdbViewer: A historical perspective. Electrophoresis, 30(S1), S162-S173. 35. Gupta, O. P., & Rani, S. (2010). Bioinformatics applications and tools: An overview. CiiT-International Journal of Biometrics and Bioinformatics, 3(3), 107-110. 36. Gupta, O. P. (2017). Study and analysis of various bioinformatics applications using protein BLAST: an overview. Advances in Computational Sciences and Technology, 10(8), 2587-2601. 37. Helmy, M., Crits-Christoph, A., & Bader, G. D. (2016). Ten simple rules for developing public biological databases. PLoS computational biology, 12(11), e1005128. 38. https://academic.oup.com/nar/article-abstract/36/suppl_1/D190/2507561 39. https://academic.oup.com/nar/article-abstract/37/suppl_1/D169/1003732 40. https://academic.oup.com/nar/article-abstract/38/suppl_1/D142/3112216 41. https://academic.oup.com/nar/article-abstract/41/D1/D43/1055867 42. https://academic.oup.com/nar/article-abstract/42/D1/D191/1053513 43. https://academic.oup.com/nar/article-abstract/45/D1/D158/2605721 44. https://academic.oup.com/nar/article-abstract/49/D1/D480/6006196 45. Ismail, H. D. (2022). Bioinformatics: a practical guide to NCBI databases and sequence alignments. Chapman and Hall/CRC. 46. Jimenez-Lopez, J. C., Gachomo, E. W., Sharma, S., & Kotchoni, S. O. (2013). Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases. 47. Kapetanovic, I. M., Rosenfeld, S., & Izmirlian, G. (2004). Overview of commonly used bioinformatics methods and their applications. Annals of the New York Academy of Sciences, 1020(1), 10-21. 48. Karp, P. D., Paley, S., & Zhu, J. (2001). Database verification studies of SWISS-PROT and GenBank. Bioinformatics, 17(6), 526-532. 49. Kehoe, K. (2019). Specialized databases in molecular biology and genetics: the nucleic acid and protein sequence databases. In Electronic Information Systems in Sci-Tech Libraries (pp. 99-125). Routledge. 50. Kodama, Y., Mashima, J., Kaminuma, E., Gojobori, T., Ogasawara, O., Takagi, T., ... & Nakamura, Y. (2012). The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. Nucleic acids research, 40(D1), D38-D42. 51. Kodama, Y., Mashima, J., Kosuge, T., Kaminuma, E., Ogasawara, O., Okubo, K., ... & Takagi, T. (2018). DNA data bank of Japan: 30th anniversary. Nucleic acids research, 46(D1), D30-D35. 52. Korf, I., Yandell, M., & Bedell, J. (2003). Blast. O'Reilly Media, Inc.. 53. Kukkonen-Macchi, A., Hautaniemi, S., Heil, K. F., Heinäniemi, M., Jensen, L. J., Junttila, S., ... & Elo, L. L. (2024). ECCB2024: The 23rd European Conference on Computational Biology. Bioinformatics, 40(Supplement_2), ii1-ii3. 54. Kumar, A. Introduction to biological databases. Recent Advances in Chemical Sciences and Biotechnology, 25. 55. Lakshmi, P., & Ramyachitra, D. (2020). Review about bioinformatics, databases, sequence alignment, docking, and drug discovery. In Statistical modelling and machine learning principles for bioinformatics techniques, tools, and applications (pp. 11-23). Singapore: Springer Singapore. 56. Lakshmi, P., & Ramyachitra, D. (2020). Review about bioinformatics, databases, sequence alignment, docking, and drug discovery. In Statistical modelling and machine learning principles for bioinformatics techniques, tools, and applications (pp. 11-23). Singapore: Springer Singapore. 57. Lapatas, V., Stefanidakis, M., Jimenez, R. C., Via, A., & Schneider, M. V. (2015). Data integration in biological research: an overview. Journal of Biological Research-Thessaloniki, 22(1), 9. 58. Lavenier, D., & Giraud, M. (2005). Bioinformatics applications. In Reconfigurable Computing: Accelerating Computation with Field-Programmable Gate Arrays (pp. 157-182). Boston, MA: Springer US. 59. Ludwig, W. (1995). Sequence databases. In Molecular microbial ecology manual (pp. 309-330). Dordrecht: Springer Netherlands. 60. Madden, T. (2013). The BLAST sequence analysis tool. The NCBI handbook, 2(5), 425-436. 61. Manzano, A., Weging, S., Bezdan, D., Borg, J., Cahill, T., Carnero-Diaz, E., ... & Herranz, R. (2023). Enhancing European capabilities for application of multi-omics studies in biology and biomedicine space research. Iscience, 26(9). 62. Mashima, J., Kodama, Y., Fujisawa, T., Katayama, T., Okuda, Y., Kaminuma, E., ... & Takagi, T. (2016). DNA data bank of Japan. Nucleic Acids Research, gkw1001. 63. Mashima, J., Kodama, Y., Kosuge, T., Fujisawa, T., Katayama, T., Nagasaki, H., ... & Takagi, T. (2016). DNA data bank of Japan (DDBJ) progress report. Nucleic acids research, 44(D1), D51-D57. 64. Miyazaki, S., Sugawara, H., Gojobori, T., & Tateno, Y. (2003). DNA data bank of Japan (DDBJ) in XML. Nucleic Acids Research, 31(1), 13-16. 65. Miyazaki, S., Sugawara, H., Ikeo, K., Gojobori, T., & Tateno, Y. (2004). DDBJ in the stream of various biological data. Nucleic acids research, 32(suppl_1), D31-D34. 66. Mizrachi, I., McEntyre, J., & Ostell, J. (2007). GenBank: the nucleotide sequence database. The NCBI handbook. 67. Mount, D. W. (2007). Using the basic local alignment search tool (BLAST). Cold spring harbor Protocols, 2007(7), pdb-top17. 68. Mukhopadhyay, C. S., Choudhary, R. K., & Iquebal, M. A. (2017). Basic applied bioinformatics. John Wiley & Sons. 69. NCBI Resource Coordinators. (2012). Database resources of the national center for biotechnology information. Nucleic acids research, 41(D1), D8-D20. 70. NCBI Resource Coordinators. (2012). Database resources of the national center for biotechnology information. Nucleic acids research, 41(D1), D8-D20. 71. NCBI Resource Coordinators. (2015). Database resources of the national center for biotechnology information. Nucleic acids research, 43(D1), D6-D17. 72. NCBI Resource Coordinators. (2015). Database resources of the national center for biotechnology information. Nucleic acids research, 43(D1), D6-D17. 73. Neumann, R. S., Kumar, S., & Shalchian-Tabrizi, K. (2014). BLAST output visualization in the new sequencing era. Briefings in bioinformatics, 15(4), 484-503. 74. Neumann, R. S., Kumar, S., Haverkamp, T. H. A., & Shalchian-Tabrizi, K. (2014). BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data. BMC bioinformatics, 15(1), 128. 75. Oehmen, C., & Nieplocha, J. (2006). ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis. IEEE Transactions on Parallel and Distributed Systems, 17(8), 740-749. 76. Okido, T., Kodama, Y., Mashima, J., Kosuge, T., Fujisawa, T., & Ogasawara, O. (2022). DNA Data Bank of Japan (DDBJ) update report 2021. Nucleic acids research, 50(D1), D102-D105. 77. O'Cathail, C., Ahamed, A., Burgin, J., Cummins, C., Devaraj, R., Gueye, K., ... & Cochrane, G. (2025). The european nucleotide archive in 2024. Nucleic Acids Research, 53(D1), D49-D55. 78. PAWAR, A., PATIL, J., & JADHAV, R. INTRODUCTION TO BASIC BIOINFORMATIC TOOLS. LIFE SCIENCES: TRENDS AND TECHNOLOGY, 1. 79. Persson, B. (2000). Bioinformatics in protein analysis. Proteomics in functional genomics: Protein structure analysis, 215-231. 80. Rehm, B. (2001). Bioinformatic tools for DNA/protein sequence analysis, functional assignment of genes and protein classification. Applied microbiology and biotechnology, 57(5), 579-592. 81. Rehm, B. (2001). Bioinformatic tools for DNA/protein sequence analysis, functional assignment of genes and protein classification. Applied microbiology and biotechnology, 57(5), 579-592. 82. Samal, K. C., Sahoo, J. P., Behera, L., & Dash, T. (2021). Understanding the BLAST (Basic Local Alignment Search Tool) program and a step-by-step guide for its use in life science research. Bhartiya Krishi Anusandhan Patrika, 36(1), 55-61. 83. Sayers, E. W., Barrett, T., Benson, D. A., Bolton, E., Bryant, S. H., Canese, K., ... & Ye, J. (2010). Database resources of the national center for biotechnology information. Nucleic acids research, 39(suppl_1), D38-D51. 84. Sayers, E. W., Barrett, T., Benson, D. A., Bolton, E., Bryant, S. H., Canese, K., ... & Ye, J. (2010). Database resources of the national center for biotechnology information. Nucleic acids research, 39(suppl_1), D38-D51. 85. Schmidt, C. W. (2003). Data explosion: bringing order to chaos with bioinformatics. Environmental health perspectives, 111(6), A340-A345. 86. Schneider, M., Tognolli, M., & Bairoch, A. (2004). The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools. Plant Physiology and Biochemistry, 42(12), 1013-1021. 87. Sharma, M. K., Dhar, M. K., & Kaul, S. (2012). Bioinformatics: An introduction and overview. 2012 International Journal of Engineering Research and Development, 3(8), 88-99. 88. Sharma, P. K., & Yadav, I. S. (2022). Biological databases and their application. In Bioinformatics (pp. 17-31). Academic Press. 89. Sharma, T. R., SHARMA, S., & SHARMA, S. BIOINFORMATICS AN OVERVIEW. ADVANCED SCIENCE: A FUTURISTIC APPROACH, 82(91), 9. 90. SIB Swiss Institute of Bioinformatics Members. (2016). The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic acids research, 44(D1), D27-D37. 91. Singh, B. D., & Singh, A. K. (2015). Bioinformatics tools and databases for genomics research. In Marker-Assisted Plant Breeding: Principles and Practices (pp. 401-429). New Delhi: Springer India. 92. Sivakumar, K. (2007). Protein sequence analysis and characterization using Insilico methods. Medical Biotechnology. Aavishkar Publisher; Jaipur, 211-235. 93. Soudy, M., Anwar, A. M., Ahmed, E. A., Osama, A., Ezzeldin, S., Mahgoub, S., & Magdeldin, S. (2020). UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase). Journal of Proteomics, 213, 103613. 94. Syngai, G. G., Barman, P., Bharali, R., & Dey, S. (2013). BLAST: An introductory tool for students to Bioinformatics Applications. Keanean Journal of Science, 2, 67-76. 95. Tanizawa, Y., Fujisawa, T., Kodama, Y., Kosuge, T., Mashima, J., Tanjo, T., & Nakamura, Y. (2023). DNA Data Bank of Japan (DDBJ) update report 2022. Nucleic acids research, 51(D1), D101-D105. 96. Tateno, Y., Imanishi, T., Miyazaki, S., Fukami-Kobayashi, K., Saitou, N., Sugawara, H., & Gojobori, T. (2002). DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic acids research, 30(1), 27-30. 97. Tateno, Y., Miyazaki, S., Ota, M., Sugawara, H., & Gojobori, T. (2000). DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucleic Acids Research, 28(1), 24-26. 98. Taylor, R. C. (2010). An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. BMC bioinformatics, 11(Suppl 12), S1. 99. Thakur, M., Bateman, A., Brooksbank, C., Freeberg, M., Harrison, M., Hartley, M., ... & McEntyre, J. (2023). EMBL's European bioinformatics institute (EMBL-EBI) in 2022. Nucleic Acids Research, 51(D1), D9-D17. 100. UniProt Consortium. (2007). The universal protein resource (UniProt). Nucleic acids research, 36(suppl_1), D190-D195. 101. UniProt Consortium. (2009). The universal protein resource (UniProt) 2009. Nucleic acids research, 37(suppl_1), D169-D174. 102. UniProt Consortium. (2010). Ongoing and future developments at the Universal Protein Resource. Nucleic acids research, 39(suppl_1), D214-D219. 103. UniProt Consortium. (2010). The universal protein resource (UniProt) in 2010. Nucleic acids research, 38(suppl_1), D142-D148. 104. UniProt Consortium. (2012). Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic acids research, 40(D1), D71-D75. 105. UniProt Consortium. (2012). Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic acids research, 41(D1), D43-D47. 106. UniProt Consortium. (2014). Activities at the universal protein resource (UniProt). Nucleic acids research, 42(D1), D191-D198. 107. Wheeler, D. L., Church, D. M., Lash, A. E., Leipe, D. D., Madden, T. L., Pontius, J. U., ... & Rapp, B. A. (2001). Database resources of the national center for biotechnology information. Nucleic acids research, 29(1), 11-16. 108. Wu, C. H. (2003). The Protein Information Resource for Functional Genomics and Proteomics. In Computational Biology and Genome Informatics (pp. 117-137). 109. Yan, Q. (2008). Bioinformatics databases and tools in virology research: an overview. In silico biology, 8(2), 71-85. 110. Yan, Q. (2008). Bioinformatics databases and tools in virology research: an overview. In silico biology, 8(2), 71-85. 111. Yan, Q. (2008). Bioinformatics databases and tools in virology research: an overview. In silico biology, 8(2), 71-85. \ 112. Yekta, R. F., & Arefi Oskouie, A. (2018). Biological databases. In Genomic Approach to Asthma (pp. 303-337). Singapore: Springer Singapore. 113. Yuan, D., Ahamed, A., Burgin, J., Cummins, C., Devraj, R., Gueye, K., ... & Cochrane, G. (2024). The European nucleotide archive in 2023. Nucleic acids research, 52(D1), D92-D97.