PPT-Alternative splicing: Sequence Alignment

with Affine Gap Erin Howell Alternative Splicing Identifying alternative splicing sites with an alignment Look for patterns in gene splicing Use affine gap to identify splice sites Data ATF3 . 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. Genome Alignment in the Human Genome. Jian. Ma. Jian Ma | Sequence Comparison and Genome Alignment | 2015. 1. PowerPoint by Casey . Hanson. Introduction. This goals of the lab are as follows:. Gain experience using BLAST and Genome Browsers by looking at repeat families in the VHL gene.. 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. AGRY 600 2014. What exactly are we talking about?. Constitutive splicing = all possible introns removed. Alternative splicing (AS): . a single gene can encode many messages depending on how the . initial transcript is spliced. SUBMITTED BY. . SELMA ABDUL SAMAD. . BCH-10-05-02. . S3 . MSc. BIOCHEMISTRY. Interrupted Genes. Prokaryotes. – continuous gene(uninterrupted) . Eukaryotes. – gene is interrupted with non-coding 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. Integrins. Alyssa Schwartz. Group Meeting . 11-30-15. Splicing is an Essential Step in the Central Dogma. Pearson, Prentice Hall. Types of Splice . Variations. Claude C. . Warzecha. , . Russ P. . Carstens. 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:. BIOS 234. June 1. Variant Detection Pipeline. Alignment. Variant Discovery and Genotyping. Prioritization and Filtering. Variant Interpretation. DNA Sequencing. Functional Validation / Clinical Assessment. 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 . eucaryotes. and bacteria.. The final level of a protein in the cell depends on the efficiency of each step and on the rates of degradation of the RNA and protein molecules. (A) In . eucaryotic. cells the RNA molecule produced by transcription alone (sometimes referred to as the primary transcript) would contain both coding (. 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 .