PPT-Gapped BLAST and PSI-BLAST : a new generation of protein database search programs

Team2 邱冠儒 黃 尹 柔 田 耕 豪 蕭 逸 嫻 謝朝茂 莊閔 傑 20140512 1 BLAST Basic local alignment search tool Enable to compare query sequence of aminoacid or protein or DNA to database . Sequence Alignment . Concepts. Introduction to Biostatistics and Bioinformatics. Sequence . Database Searching. This Lecture. Stuart M. Brown, Ph.D.. Center for Health Informatics and Bioinformatics. 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. Psi BLAST, . Perl: Arrays, . Loops, Hashes . J. Peter Gogarten . Office:. BPB 404. phone:. 860 486-4061, . Email:. . gogarten@uconn.edu. Blast: find High Scoring Pairs between query and database of target sequences. Psi BLAST, . Perl: Arrays, Loops . J. Peter Gogarten . Office:. BPB 404. phone:. 860 486-4061, . Email:. . gogarten@uconn.edu. Psi-Blast: Detecting structural homologs. Psi-Blast was designed to detect homology for highly divergent amino acid sequences. Selection. Allele frequency. 0. 100. advantageous. disadvantageous. Modified from from . www.tcd.ie/Genetics/staff/Aoife/GE3026/GE3026_1+2.ppt. . Purifying selection in GTA genes. dN/dS <1 for GTA genes has been used to infer selection for function. Mohammed Mehdi Rizvi. Molecular Lab Techniques 446. Background. BLAST is the . B. asic . L. ocal . A. lignment . S. earch . T. ool. . It is an algorithm used for comparing sequences, such as amino acid sequences of proteins, or the nucleotides of DNA sequences.. 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. Adapted from College Board’s “Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST”. What we know so far.... We already know that DNA can be used to identify animal species at a genetic level. hex 27 0180 Diaphragm pressure swit0180 Outline. A brief introduction on various kind of BLAST. Different Sequences: introduction of NCBI and FASTA format. Web version BLAST. BLAST on Linux system. An application of BLAST on Bioengineering.   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 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. . 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..