PPT-Basic Local Alignment Search Tool

Altschul etal 1990 傅安 陳岳昇 陳宗涵 20161212 Outline Introduction and Methods Results Conclusion Introduction Measures of similarity between sequences to distinguish biologically significant relationships. Basic Local Alignment Search Tool Stephen F Altschul Warren Gish Webb Miller2 Eugene W Myers3 and David J Lipmanl Satwnal Center for Biotechnology Informalion Kdional Library of Medicine National Insti 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. output. How to . measure. the similarity between two sequences. Q: which one is a better match to the query ?. Query: . M. . A T. . W . L. . . Seq_A: . M. . A T. P P . Seq_B: . M. P P . W . and. Continuous Search. Local search algorithms. In many optimization problems, the . path . to the goal is irrelevant; the goal state itself is the . solution. In such cases, we can use . local search algorithms. Jeremy Buhler (. in absentia. ). Wilson Leung 07/2015. Key limitations of the . Smith. -Waterman . local. alignment algorithm. Quadratic. . in time and space complexity. Report only . one optimal alignment. Do Huy Hoang. Sequence Alignment. Sequence Similarity. Alignment. Arrange DNA/Protein sequences to show the similarity. “” denotes the insertion/deletion event. Other variations. Edit distance. 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:. 1A BUSINESS-LEDSTATEWIDEITOGROWANDDIVERSIFYTHEPRIVATESECTORINEACHVIRGINIAREGION2PER CAPITA FUNDING7 proposals submitted4 out of 9 regions participated1 Commercialization3 Talent Development3 Infrastru 1. Data structure: Lookup Table. Application: BLAST . 2. The Look-up Table Data Structure. A . k-mer . is a string of length . k.. A . lookup table. is a table of size . |. Σ. |. k. . that stores the location of all . ). Design. Curation. Data Mining. Computational Biology. . Tools for:. Sequence analysis. Structure prediction. Docking. Structural genomics. Functional genomics. Proteomics . Interactomics. BIOINFORMATICS. Hardison. Genomics 4_1. Sources: Webb Miller (Penn State. ). Kun-Mao Chao and . Luxin. Zhang: . Sequence Comparisons, Theory . and Methods. , Springer 2008. Bill Pearson (U. Virginia). Vladimir . Lukic. Outline I ntroduction BLAST s earch s teps Step 1: Specifying Sequence of interest Step 2: Selecting BLAST Program Step 3: Selecting a Database Step 4: Selecting Search Parameters and Format Post-Doctoral Fellow. Ochman. Lab. Global . vs. Local Alignments. Global . . The global approach is useful when you are comparing a small group of sequences, but becomes become computationally expensive as the number of sequence in the comparison increases. . Laboratory of Mathematical Chemistry,. Bourgas University “Prof. Assen Zlatarov”. Bulgaria. 2. What is Query Tool?. Environmental fate - examples (BCF, BOD) . Human health hazard - examples (AMES and Carcinogenicity) .