Bioinformatics is a scientific subdiscipline involving computational technology to analyze biological data such as DNA sequencing, protein analysis, and gene expression. After the biological data is found in a wet lab it is stored and organized in a database before various software algorithms and tools analyze the data. A common task these algorithms accomplish is sequencing the alignment where DNA, RNA, or protein sequences are compared to find any similarities or differences to show any evolutionary relationships or potential functions. Bioinformatic tools are also able to create visual representations of charts and graphs to better help scientists understand the data. After the data is analyzed and visualized, bioinformaticians interpret the results in the context of existing biological knowledge, which leads to discoveries about genes, diseases, and biological processes.
Types of Algorithms:
The Needleman-Wunsch algorithm was based on dynamic programming and guarantees finding the optimal alignment of sequence pairs. It essentially divides the full sequence into a series of shorter sequence segments and uses the solutions of the smaller problem to construct a solution to the large problem. The similarities found in the sequences are put into a matrix and the algorithm finds the gaps in the sequence alignment. Although this method does guarantee an accurate result, it is too slow to use to probe a large sequence database.
PSI-BLAST (Position-Specific Iterative Basic Local Alignment Search Tool), is a bioinformatics tool that is based on the speed of BLAST (Basic Local Alignment Search Tool) but improved to be able to find more distantly related sequences with higher sensitivity. The PSI-BLAST will start by performing a regular BLAST search on the sequence database to identify any sequences with significant alignments. It will then construct a profile called PSSM based on the high-scoring sequences identified in the initial BLAST search. Essentially learning which patterns are the most likely to be important for function within the family of sequences provided. PSI-BLAST will then use the PSSM and run another BLAST search against the database. This will lead to a more refined result allowing the algorithm PSI-BLAST to identify more distantly related sequences that share these conserved patterns.
Bioinformatics transforms complex biological data into something computers can analyze which in turn can provide bioinformatics insights. By continuing research with algorithms like Needleman-Wunsch for precision and PSI-BLAST for sensitive detection of distantly related sequences, bioinformaticians can unlock a deeper understanding of genes, diseases, and biological processes. As technology continues to improve bioinformatics will undoubtedly contribute to the progression of research.
References
Lesk, Arthur M. “Bioinformatics.” Encyclopædia Britannica, Encyclopædia Britannica, inc., 24 May 2024, www.britannica.com/science/bioinformatics.
Luscombe, N.M., et al. Review What Is Bioinformatics? An Introduction and Overview, Yale University, 2001, www.thiemeconnect.com/products/ejournals/pdf/10.1055/s-0038-1638103.pdf.
Bhagwat, Medha, and L. Aravind “Psi-Blast Tutorial.” Comparative Genomics: Volumes 1 and 2., U.S. National Library of Medicine, 1 Jan. 1970, www.ncbi.nlm.nih.gov/books/NBK2590/.
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