PPT-Previous Lecture: Sequence Alignment

Concepts Introduction to Biostatistics and Bioinformatics Sequence Database Searching This Lecture Stuart M Brown PhD Center for Health Informatics and Bioinformatics NYU School of Medicine. Sequence Alignment . Concepts. Introduction to Biostatistics and Bioinformatics. Sequence . Database Searching. This Lecture. Stuart M. Brown, Ph.D.. Center for Health Informatics and Bioinformatics. Hypothesis Tesing 2: Comparing Samples. Multiple Alignment. Stuart M. Brown. NYU School of Medicine. Learning Objectives. Understand the need for multiple alignment methods in biology. Optimal methods (dynamic programming) are not practical to align many sequences. Jia. -Ming Chang, Paolo Di . Tommaso. , and Cedric . Notredame. TCS. : A new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree . reconstruction, . Probability. Introduction to Biostatistics and Bioinformatics. Sequence Alignment Concepts . This Lecture. Sequence Alignment. Stuart M. Brown, Ph.D.. Center for Health Informatics and Bioinformatics. Scott Walmsley, PhD. Research Instructor, Department Pharmaceutical Sciences. Skaggs School of Pharmacy. Outline . What is and why perform Multiple . S. equence . A. lignment (MSA)?. Pre-requisite knowledge. identity vs. similarity. homology vs. similarity. gap penalty. affine gap penalty. gap penalty high. fewer gaps, if investigating related sequences . low. more gaps, larger gaps, distantly related sequences. Tandy Warnow. The Department of Computer Science. The University of Texas at Austin. The “Tree of Life”. Avian Phylogenomics Project. G Zhang, . BGI. . Approx. 50 species, whole genomes. 8000+ genes, UCEs. Maya Schushan. November 2010. Outline- introduction to alignments. 1. . Introduction. 4. Pairwise Alignment:. Smith-Waterman. Needlman-Wunch. 5. Multiple Sequence Alignment:. ClustalW. MUSCLE. T-coffee. BMI 877. Colin Dewey. colin.dewey@wisc.edu. March 14, 2017. Overview. What does it . mean . to . align. sequences?. How do we cast sequence alignment as a . computational problem?. What . algorithms . Jia. -Ming Chang, Paolo Di . Tommaso. , and Cedric . Notredame. TCS. : A new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree . reconstruction, . Niroula. Department of Experimental Medical Science. Lund University. 1. 2015-12-09. Sequence alignment. A way of arranging . two or more sequences . to identify regions of . similarity. Shows locations of similarities and differences between . Introduction to Biostatistics and Bioinformatics. Sequence Alignment Concepts . This Lecture. Sequence Alignment. Stuart M. Brown, Ph.D.. Center for Health Informatics and Bioinformatics. NYU School of Medicine. pair-wise alignment. × . multiple . sequence . alignment. Flavors of sequence alignment. global alignment . × . local alignment. global. local. align entire sequence. stretches of sequence with the highest density of matches . the role of gene duplication followed by loss of function in speciation. For Friday, go through the slides from class 11. Aligning sequences is part of many analytical pipelines . Alignments can be local or global.