PPT-Blast Basic Local Alignment Search Tool

Recap Pairwise sequence alignment Grouping of two sequences to maximize similarityidentity using a scoring system substitution matrices PAM 1120250 BLOSUM 806245 Optimal alignment algorithms. Sequence Alignment . Concepts. Introduction to Biostatistics and Bioinformatics. Sequence . Database Searching. This Lecture. Stuart M. Brown, Ph.D.. Center for Health Informatics and Bioinformatics. 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 . 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. Thermo Fisher / Open Biosystems. Dr. Krishnan K. . Chittur. University of Alabama in Huntsville. Dr. Joseph Ng. University of Alabama in Huntsville. What is BLAST. B.L.A.S.T. stands for . B. asic . L. Jia. -Ming Chang, Paolo Di . Tommaso. , and Cedric . Notredame. TCS. : A new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree . reconstruction, . 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 . Concepts. Introduction to Biostatistics and Bioinformatics. Sequence . Database Searching. This Lecture. Stuart M. Brown, Ph.D.. Center for Health Informatics and Bioinformatics. NYU School of Medicine. BLAST. Local pairwise alignment heuristic. Faster than standard pairwise alignment programs such as SSEARCH, but less sensitive.. Online server: . http://www.ncbi.nlm.nih.gov/blast. BLAST. Given a query . 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.. ). Design. Curation. Data Mining. Computational Biology. . Tools for:. Sequence analysis. Structure prediction. Docking. Structural genomics. Functional genomics. Proteomics . Interactomics. BIOINFORMATICS.   Understanding the BLAST (Basic Local Alignment Search Tool) Program and a Step-by-step Guide for its use in Life Science Research Kailash Chandra Samal, Jyoti Prakash S 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 Just a reminder of the important concept in sequence analysis – . homology. . It is a conclusion about a common ancestral relationship drawn from sequence similarity.. Sequence . similarity. is a direct result of observation from the sequence alignment. It can be quantified using percentages, but homology can not!. Altschul. . et.al. , 1990. . 傅安. . 陳岳昇. . . 陳宗涵. 2016.12.12. Outline. Introduction and Methods. Results. Conclusion. Introduction. Measures of similarity between sequences to distinguish biologically significant relationships..