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- Title
Clinical bioinformatics. Part II: A software-aided approach.
- Authors
Dumitrescu, Iolanda
- Abstract
Biocomputing tool development is at the basis of all bioinformatics analysis. It means writing software for sequence, structural, functional analysis, the construction and management of biological databases. Sequence comparison is becoming of great importance to get functional and evolutionary inference of a new sequence with sequences already existing in biological databases. Pairwise sequence alignment is to find the optimum pairing of two sequences, so that there should be the best correspondence among residues. The existing alignment algorithms, based either on a global or a local strategy, differ only in the optimization strategy used in aligning similar residues. In retrieving biological sequences in databases based on similarity, exhaustive algorithms lead to a best or exact solution by examining all mathematical combinations, but they are computationally very intensive. Heuristic algorithms are rather a computational strategy to find an empirical or near optimal solution in a realistic time frame. In multiple sequence alignment, sequences are aligned so that a maximum number of residues from each sequence are matched up according to a particular scoring function. Exhaustive approaches involve examining all possible aligned positions simultaneously, but at the expense of computational time and memory space required. To alleviate that, heuristic approaches have been developed: progressive alignment, iterative alignment, block-based alignment. Using bioinformatics software it is necessary to make a compromise between accuracy and computational feasibility. Accurate results can be obtained if one draws a consensus by comparing the output from different programs implementing algorithms that satisfy the computational conditions. The application of bioinformatics in cancer research is still in an early stage; it has already become an obligatory technology to assist and improve the development of cancer therapy in the post-genomic era.
- Subjects
BIOLOGICAL databases; BIOINFORMATICS software; BIOINFORMATICS; SEQUENCE alignment; HEURISTIC algorithms
- Publication
Oncolog-Hematolog, 2020, Issue 52, p39
- ISSN
2066-8716
- Publication type
Article