{"product_id":"local-alignment-and-statistics","title":"Local Alignment and Statistics","description":"\u003cp\u003eThis course, from the MIT Open Courseware library, provides an overview of the principles and tools used in classical and next-generation sequencing. The second half of the course covers BLAST- Basic Local Alignment Search Tool- which is an algorithm that allows a researcher to compare a query sequence with a larger set of sequences. This course is the second lecture in a larger Foundations of Computational and Systems Biology course taught at MIT in Spring 2014.\u003c\/p\u003e\n\u003cp\u003e \u003c\/p\u003e\n\u003cmeta charset=\"utf-8\"\u003e\n\u003ch3\u003eLearning Objectives:\u003c\/h3\u003e\n\u003cul\u003e\n\u003cli\u003e\u003cstrong\u003eDescribe the process of conventional sequencing technologies\u003c\/strong\u003e\u003c\/li\u003e\n\u003cli\u003e\u003cstrong\u003eDefine the Sanger Sequencing method\u003c\/strong\u003e\u003c\/li\u003e\n\u003cli\u003e\u003cstrong\u003eIdentify examples and characteristics of conventional sequencing technologies\u003c\/strong\u003e\u003c\/li\u003e\n\u003cli\u003e\u003cstrong\u003eDistinguish between various next generation sequencing technologies\u003c\/strong\u003e\u003c\/li\u003e\n\u003cli\u003e\u003cstrong\u003eHighlight the benefits of local alignment\u003c\/strong\u003e\u003c\/li\u003e\n\u003cli\u003e\u003cstrong\u003eDevelop a BLAST-like algorithm\u003c\/strong\u003e\u003c\/li\u003e\n\u003cli\u003e\u003cstrong\u003eDefine statistics of matching\u003c\/strong\u003e\u003c\/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eTarget frequencies and mismatch penalties for nucleotide alignments\u003c\/strong\u003e \u003c\/li\u003e\n\u003c\/ul\u003e\n\u003cmeta charset=\"utf-8\"\u003e\n\u003col class=\"sections\"\u003e\n\u003cli\u003e\n\u003ch3\u003eOverview - \u003cspan style=\"color: #ff0000;\"\u003e3 minutes\u003c\/span\u003e\n\u003c\/h3\u003e\n\u003col class=\"collapsable-container\"\u003e\n\u003cli class=\"file video\"\u003eWhat do you already know?\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eOverview and objectives\u003c\/li\u003e\n\u003c\/ol\u003e\n\u003c\/li\u003e\n\u003cli\u003e\n\u003ch3\u003eConventional Sequencing - \u003cspan style=\"color: #ff0000;\"\u003e10 minutes\u003c\/span\u003e\n\u003c\/h3\u003e\n\u003col class=\"collapsable-container\"\u003e\n\u003cli class=\"file video\"\u003e1D, 2D, and 3D models of DNA\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eSanger Sequencing Method\u003c\/li\u003e\n\u003cli class=\"file video\"\u003ePractical Examples of Conventional Sequencing\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eRead Lengths of Conventional Sequencing\u003c\/li\u003e\n\u003c\/ol\u003e\n\u003c\/li\u003e\n\u003cli\u003e\n\u003ch3\u003eNext Gen Sequencing - \u003cspan style=\"color: #ff0000;\"\u003e10 minutes\u003c\/span\u003e \u003c\/h3\u003e\n\u003col class=\"collapsable-container\"\u003e\n\u003cli class=\"file video\"\u003eNext Generation Sequencing Technologies\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eRoche Technology\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eIllumina Technology\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eHelicose and Pac Bio Technologies\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eDeeper Dive into Roche Technology\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eDeeper Dive into Illumina Technology\u003c\/li\u003e\n\u003c\/ol\u003e\n\u003c\/li\u003e\n\u003cli\u003e\n\u003ch3\u003eLocal Alignment - \u003cspan style=\"color: #ff0000;\"\u003e15 minutes\u003c\/span\u003e\n\u003c\/h3\u003e\n\u003col class=\"collapsable-container\"\u003e\n\u003cli class=\"file video\"\u003eWhy Align Sequences?\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eFinding Top Scoring Alignment Matches\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eCreating an Algorithm to Find Top Matches\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eCalculating Running Time\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eExpected Score Has to Be Negative\u003c\/li\u003e\n\u003c\/ol\u003e\n\u003c\/li\u003e\n\u003cli\u003e\n\u003ch3\u003eDeeper Dive into the Algorithm  - \u003cspan style=\"color: #ff0000;\"\u003e10 minutes\u003c\/span\u003e\n\u003c\/h3\u003e\n\u003col class=\"collapsable-container\"\u003e\n\u003cli class=\"file video\"\u003eIdentifying Frequency of High Scoring Segments Across a Sequence\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eCalculating Lambda\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eWhat Happens to Lambda If Scores Are Doubled? \u003c\/li\u003e\n\u003cli class=\"file video\"\u003eWhat Does Lambda Mean?\u003c\/li\u003e\n\u003c\/ol\u003e\n\u003c\/li\u003e\n\u003cli\u003e\n\u003ch3\u003eScoring Matrix and Mismatch Penalty - \u003cspan style=\"color: #ff0000;\"\u003e8 minutes\u003c\/span\u003e\n\u003c\/h3\u003e\n\u003col class=\"collapsable-container\"\u003e\n\u003cli class=\"file video\"\u003eWhat Scoring Matrix to Use for DNA\u003c\/li\u003e\n\u003cli class=\"file video\"\u003eChoosing the Mismatch Penalty\u003c\/li\u003e\n\u003c\/ol\u003e\n\u003c\/li\u003e\n\u003cli\u003e\n\u003ch3\u003eWrap Up - \u003cspan style=\"color: #ff0000;\"\u003e2 minutes\u003c\/span\u003e\n\u003c\/h3\u003e\n\u003col class=\"collapsable-container\"\u003e\n\u003cli class=\"file quiz\"\u003eWhat Do You Know Now?\u003c\/li\u003e\n\u003c\/ol\u003e\n\u003c\/li\u003e\n\u003c\/ol\u003e\n\u003cp\u003e \u003c\/p\u003e","brand":"Learning.ly","offers":[{"title":"Default Title","offer_id":6928752385,"sku":"","price":0.0,"currency_code":"GBP","in_stock":true}],"thumbnail_url":"\/\/cdn.shopify.com\/s\/files\/1\/0817\/1429\/products\/imAlMOjfShCFdNP0iQkN.jpeg?v=1443621467","url":"https:\/\/piers-test-store.myshopify.com\/products\/local-alignment-and-statistics","provider":"The Test Store","version":"1.0","type":"link"}