PPT-Sequences and Alignment Format

Galaxy overview and Interface Getting Data in Galaxy Analyzing Data in Galaxy Quality Control Mapping Data History and workflow Galaxy Exercises https galaxybioinfoucredu NGS Analysis Using Galaxy. Tandy Warnow. The Department of Computer Science. The University of Texas at Austin. Metagenomic. . Taxon. . Identification. Objective: classify short reads in a metagenomic sample. 1. . What. is . 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. Utah State University – Spring . 2012. STAT 5570: Statistical Bioinformatics. Notes 6.1. 2. References. Chapters 2 & 7 of Biological Sequence Analysis (Durbin et al., 2001). . 3. Review. Genes are:. and Sequence Profiles. Multiple sequence alignment. Generalize our pairwise alignment of sequences to include . more than two. homologous proteins.. Looking at more than two sequences gives us . much more information. 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. June 16, 2016. Michael Nute. 1. BAli-Phy: Brief Summary. What is . BAli-Phy? . (Redelings & . Suchard. , 2005). Software from 2005 that takes as input unaligned sequences and co-estimates the alignment and the phylogeny in a way that accounts for . Multiple Sequence Alignment using Fast Fourier Transform. Intro. 2-Step Procedure. Homology Identification using FFT. Alignment Scoring/Selection. Faster computation due to…. Approx. O(NlogN) homology detection. and . pairwise. alignments. 1. “. It is a capital mistake to theorize before one has data. Insensibly one begins to twist facts to suit theories, instead of theories to suit facts.. ” . (. A. Conan Doyle, . 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. Formulas booklet page 3. In maths, we call a list of numbers in order a . sequence. .. Each number in a sequence is called a . term. .. 4, 8, 12, 16, 20, 24, 28, 32, . . .. 1. st. term. 6. th. term. Hsin. -Yu Chang. www.ebi.ac.uk. Classifying . proteins into families and . identifying . protein homologues can help scientists . to . characterise. unknown proteins. . . . Greider. and Blackburn discovered telomerase in 1984 and were awarded Nobel prize in 2009. Which model organism they used for this study ? . Evolution occurs through a set of modifications to the DNA. These modifications include point mutations, insertions, deletions, and rearrangements. Seemingly diverse species (say mice and humans) share significant similarity (80-90%) in their genes. Yu He. 04/13/2016. Adapted from the multiple sequence alignment presentations . by . Mingchao. . Xie. and Julie Thompson. Last update: 08/09/2021. Multiple sequence alignments. Multiple Sequence Alignment .