PPT-Multiple Sequence Alignment

with PASTA Michael Nute Austin TX June 17 2016 Agenda Quick recap of PASTA Algorithm Run the GUI Explore GUI options and what they do in terms of PASTA Run a test alignment Explore PASTA outputs and diagnostics. Linear-space alignment. Using 2 columns of space, we can compute. for k = 1…M, F(M/2, k), F. r. (M/2, N – k). . PLUS the backpointers. x. 1. …. x. M/2. y. 1. x. M. y. N. x. 1. …. x. M/2+1. 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. 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. 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:. Xuhua Xia. xxia@uottawa.ca. http://dambe.bio.uottawa.ca. Xuhua Xia. Slide . 2. Normal and Thalassemia HBb. Are the two genes homologous?. What evolutionary change can you infer from the alignment? . What is the consequence of the evolutionary change?. . You have learned about:. Data & databases. Tools . Amino Acids. Protein Structure. Today we will discuss: . Aligning sequences. After this: . You know how to perform structural alignments. BIOS 234. June 1. Variant Detection Pipeline. Alignment. Variant Discovery and Genotyping. Prioritization and Filtering. Variant Interpretation. DNA Sequencing. Functional Validation / Clinical Assessment. Places residues in columns . per . position specific similarity scores . reflects . relationships . of the . sequences. the scores are based on . indels. (gaps) and substitutions.. The alignment of residues implies that they have similar roles in the proteins or DNA sequences being aligned . Tandy . Warnow. Studies we will discuss. Katoh. and . Standley. , MBE 2013 (about MAFFT). Nelesen. et al., PSB 2008 (Impact of guide tree). Liu and Warnow, . PLoS. ONE 2012 (about treelength criteria). 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. 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 . 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 .