PPT-MCB 3421 Class 13 Multiple sequence alignment

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. 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. a case study on transmembrane protein. Jia-Ming Chang. 2013-July-09. Chang, J-M, P Di Tommaso, J-. Fß. Taly, C Notredame. 2012. Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. BMC Bioinformatics 13.. 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. s. tudent evaluations. Please follow this link to the on-line surveys . that . are open for you this semester.. . the gradualist point of view. Evolution occurs within populations where the fittest organisms have a selective advantage. Over time the advantages genes become fixed in a population and the population gradually changes. . 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?. 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. . 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. 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 . Please go to husky CT and complete student evaluations !. PSI . (. position-specific iterated) . BLAST. The NCBI page described PSI blast as follows: . “. Position-Specific Iterated BLAST (PSI-BLAST) provides an automated, easy-to-use version of a "profile" search, which is a sensitive way to look for sequence homologues. . MCB 3421 ATP binding sites – Shared Ancestry versus Convergent Evolution The most common fold in proteins is the Rossmann fold occurring in most nucleotide binding proteins. Examples are the V-/F-/A-ATPases, helicases, P-type ATPases, myosin …. 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 .