PPT-Last lecture summary Flavors of sequence alignment

pairwise 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 . 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, . New generation sequencing (NGS). The completion of human genome was just a start of modern DNA sequencing era – “high-throughput next generation sequencing” (NGS).. New approaches, reduce time and cost.. Sequencing strategies. Hierarchical genome shotgun HGS – Human Genome Project. “map first, sequence second. ”. clone-by-clone … cloning is performed twice (BAC, plasmid). Sequencing strategies. 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 . Concepts. Introduction to Biostatistics and Bioinformatics. Sequence . Database Searching. This Lecture. Stuart M. Brown, Ph.D.. Center for Health Informatics and Bioinformatics. NYU School of Medicine. Hierarchical genome shotgun HGS – Human Genome Project. “map first, sequence second. ”. clone-by-clone … cloning is performed twice (BAC, plasmid). Sequencing strategies. Whole genome shotgun WGS – Celera. 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.