PPT-CSE182-L10 Gene Finding October 09

HMM faircoin example October 09 E F H05 E L H01 06 06 04 04 1 H H T T T is the observed sequence October 09 E F H05 E L H01 06 06 04 04 0 1 06. ORFans. to . “GO”. Genomic sequence of model eukaryote . Saccharomyces cerevisiae . completed in 1996. (12.1 Mb). Despite 16 years of intense research, function of nearly 30% of putative open reading frames (ORFs) remain unknown.. 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.. BMI/CS 776 . www.biostat.wisc.edu/bmi776/. Spring . 2018. Anthony Gitter. gitter@biostat.wisc.edu. These slides, excluding third-party material, are licensed under . CC BY-NC 4.0. by Mark Craven, Colin Dewey, and Anthony Gitter. 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,. Dynamic Programming. www.cse.ucsd.edu/classes/. fa09/. cse182. www.cse.ucsd.edu/~vbafna. FA08. CSE182. Notes. Assignment 1 is online, due next Tuesday.. Discussion section is optional. Use it as a resource.. BMI/CS 776 . www.biostat.wisc.edu/bmi776/. Spring . 2018. Anthony Gitter. gitter@biostat.wisc.edu. These slides, excluding third-party material, are licensed . under . CC BY-NC 4.0. by Mark . Craven, Colin Dewey, and Anthony Gitter. Lecture 3. Gene Finding and Sequence Annotation. Objectives of this lecture. Introduce you to basic concepts and approaches of gene finding. Show you differences between gene prediction for prokaryotic and eukaryotic genomes. 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.. BMI/CS 776 . www.biostat.wisc.edu/bmi776/. Spring 2020. Daifeng. Wang. daifeng.wang@wisc.edu. These slides, excluding third-party material, are licensed . under . CC BY-NC 4.0. by Mark . Craven, Colin Dewey, Anthony . HMMs. Gene finding. April 16. Regular expressions as Protein sequence motifs. Problem: if there is a mis-match, the sequence is not accepted.. April 25, 2016. A. Fam(B). C-X-[DE]-X{10,12}-C-X-C--[STYLV]. Edward . Marcotte. , . Univ. of Texas at Austin. Lots of genes in every genome. Nature Reviews Genetics . 13:329-342 (2012). Do humans really have the biggest genomes?. Genome . size . ranges vary widely across organisms. 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.. Biology / Bioinformatics . . Edward . Marcotte. , . Univ. of Texas at Austin. Lots of genes in every genome. Nature Reviews Genetics . 13:329-342 (2012). Do humans really have the biggest genomes?.