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. Basic Local Alignment Search Tool. (Altschul et al. 1990. ). What is blast. ?. BLAST .  DNA/protein databases. GOOGLE  internet. . D. Fristrom, Boston U. .. Uses for Blast. . Identifying unknown sequence. 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 . 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. , Green, Henricks, Jones, Kennedy, . Mawhinney. , . Peluso. , Reilly, Schwartz, Shapiro, . Yanushevsky. Blast Localization and Sensing Technology. Image Courtesy of: . Stanislav. . Klabik. MOTIVATION. What is Oxy Blast?. Oxy Blast is a high quality hydrogen peroxide.. Oxy Blast is a stabilized hydrogen peroxide based product.. Oxy Blast has proprietary homeopathic ingredients to help better the health of the user.. Peptide identification. CSE182. General isotope computation. Definition:. Let p. i,a. be the abundance of the isotope with mass i Da above the least mass. Ex: P. 0,C. : abundance of C-12, P. 2,O. : O-18 etc.. 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):. HMMs. Gene finding. October 09. October 09. QUIZ!. Question:. . Your . ‘friend’ likes to gamble. . She . tosses a coin: HEADS,. she . gives you a dollar. TAILS, you give . her . a dollar.. Usually,. Dictionary Matching. Silly Quiz. Your friend has a hobby of generating random bit strings, and finding patterns in them.. One day she come to you, excited and says: I found the strangest thing in my randomly generated string; a row of of length 30 which was as follows. 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.. Team2. 邱冠儒 黃. 尹. 柔 田. 耕. 豪 蕭. 逸. 嫻 謝朝茂 . 莊閔. 傑. 2014/05/12. 1. BLAST. Basic local alignment search tool. Enable to compare query sequence of amino-acid or protein or DNA to database . 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.