PPT-FA08 CSE182 CSE 182-L2:Blast & variants I

Dynamic Programming wwwcseucsdeduclasses fa09 cse182 wwwcseucsdeduvbafna FA08 CSE182 Notes Assignment 1 is online due next Tuesday Discussion section is optional Use it as a resource. Rao CSE 326 CSE 326 Lecture 7 More on Search Trees Todays Topics Lazy Operations Run Time Analysis of Binary Search Tree Operations Balanced Search Trees AVL Trees and Rotations Covered in Chapter 4 of the text R Surg Cdr Jane Risdall . Royal Navy. Consultant. . Neuroanaesthetist/Intensivist. Senior Lecturer, Academic Dept Military . Anaesthesia. and Critical Care. Visiting Research Fellow, University of Cambridge. Yanbin Yin. Fall 2014. 1. http://. www.ncbi.nlm.nih.gov. /books/NBK52640/. 2. Why you do need to run BLAST in command line terminal?. NCBI’s server does not have a database that you want to search. 1914 and 1915, Wyndham Lewis, ed.. Percival Wyndham Lewis. 1882-1957. the men of 1914. unpopular. politics – questionable at best. artist, writer, thinker. The Enemy – and its pitfalls. Vorticism. et BLAST . avanc. é. J.. S. .. Bernardes. /H. . Richard. Mat. ériel. :. Bioinformatics and Functional Genomics. Jonathan Pevsner, . Wiley-Blackwell. ed.. Outline. Introduction. . Definition of . 03/14/2017. 1. Leonardo . Mariño-Ramírez. NCBI, NIH – Bethesda, USA. NCBI Search Services and Tools. Entrez. . integrated literature and molecular databases. Viewers. BLink. . protein similarities. , Green, Henricks, Jones, Kennedy, . Mawhinney. , . Peluso. , Reilly, Schwartz, Shapiro, . Yanushevsky. Blast Localization and Sensing Technology. Image Courtesy of: . Stanislav. . Klabik. MOTIVATION. Recap : . Pairwise. sequence alignment. Grouping of two sequences to maximize similarity/identity using a scoring system (substitution matrices):. PAM (1,120,250). BLOSUM (80,62,45). Optimal alignment algorithms:. MS applications. Microarray analysis. CSE182. LC-MS Maps. time. m/z. I. Peptide 2. Peptide 1. x x x x. x x x x x x. x x x x. x x x x x x. time. m/z. Peptide 2 elution. A peptide/feature can be labeled with the triple (M,T,I):. L8. Protein Sequence Analysis . Patterns (regular expressions). Profiles. HMM. Gene Finding. October 09. CSE 182. QUIZ!. Question:. your ‘friend’ likes to gamble. . He tosses a coin: HEADS, he gives you a dollar. TAILS, you give him a dollar.. L7. Dicitionary. . matching. Pattern matching. Fa05. CSE 182. Dictionary Matching. Q: Given k words (s. i. has length l. i. ). , . and a database of size n, find all matches to these words in the database string.. online and offline. Wen-Dar Lin. Bioinformatics core, IPMB. wdlin@gate.sinica.edu.tw. Preface. When we are talking about . sequence similarity. , we usually are talking about . local alignments. .. NCBI BLAST is one of the most famous local alignment programs where almost everyone has ever used it.. 11% of the edited variants were insertions and 4% were deletions.. RESULTS. Chromosome 29 was used to compare 1000 Bull Genomes Project run7 to local AGIL data.. 1000 Bull Genomes Project run 7 identified 149,684 variants on chromosome 29. Arya L, Rathinam SR, Lalitha P, Kim UR, Ghatani S, Tandon V. Trematode Fluke Procerovum varium as Cause of Ocular Inflammation in Children, South India. Emerg Infect Dis. 2016;22(2):192-200. https://doi.org/10.3201/eid2202.150051.