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Bioinformatics part 3 Sequence alignment introduction
 
20:09
This Bioinformatics lecture explains the details about the sequence alignment. The mechanism and protocols of sequence alignment is explained in this video lecture on Bioinformatics. For more information, log on to- http://shomusbiology.weebly.com/ Download the study materials here- http://shomusbiology.weebly.com/bio-materials.html In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.[1] Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences, such as those present in natural language or in financial data. Very short or very similar sequences can be aligned by hand. However, most interesting problems require the alignment of lengthy, highly variable or extremely numerous sequences that cannot be aligned solely by human effort. Instead, human knowledge is applied in constructing algorithms to produce high-quality sequence alignments, and occasionally in adjusting the final results to reflect patterns that are difficult to represent algorithmically (especially in the case of nucleotide sequences). Computational approaches to sequence alignment generally fall into two categories: global alignments and local alignments. Calculating a global alignment is a form of global optimization that "forces" the alignment to span the entire length of all query sequences. By contrast, local alignments identify regions of similarity within long sequences that are often widely divergent overall. Local alignments are often preferable, but can be more difficult to calculate because of the additional challenge of identifying the regions of similarity. A variety of computational algorithms have been applied to the sequence alignment problem. These include slow but formally correct methods like dynamic programming. These also include efficient, heuristic algorithms or probabilistic methods designed for large-scale database search, that do not guarantee to find best matches. Global alignments, which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size. (This does not mean global alignments cannot end in gaps.) A general global alignment technique is the Needleman--Wunsch algorithm, which is based on dynamic programming. Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context. The Smith--Waterman algorithm is a general local alignment method also based on dynamic programming. Source of the article published in description is Wikipedia. I am sharing their material. Copyright by original content developers of Wikipedia. Link- http://en.wikipedia.org/wiki/Main_Page
Views: 156685 Shomu's Biology
Genome-Wide Association Studies (2010)
 
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March 09, 2010. Karen Mohlke, Ph.D. Current Topics in Genome Analysis 2010 Handout: http://www.genome.gov/Pages/Research/IntramuralResearch/DIRCalendar/CurrentTopicsinGenomeAnalysis2010/CTGA2010_Lec08_color.pdf More: http://www.genome.gov/12514286
Dynamic programming
 
50:25
In mathematics, computer science, economics, and bioinformatics, dynamic programming is a method for solving complex problems by breaking them down into simpler subproblems. It is applicable to problems exhibiting the properties of overlapping subproblems and optimal substructure (described below). When applicable, the method takes far less time than naive methods that don't take advantage of the subproblem overlap (like depth-first search). The idea behind dynamic programming is quite simple. In general, to solve a given problem, we need to solve different parts of the problem (subproblems), then combine the solutions of the subproblems to reach an overall solution. Often when using a more naive method, many of the subproblems are generated and solved many times. The dynamic programming approach seeks to solve each subproblem only once, thus reducing the number of computations: once the solution to a given subproblem has been computed, it is stored or "memo-ized": the next time the same solution is needed, it is simply looked up. This approach is especially useful when the number of repeating subproblems grows exponentially as a function of the size of the input. This video is targeted to blind users. Attribution: Article text available under CC-BY-SA Creative Commons image source in video
Views: 374 Audiopedia

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