PPT-Using BLAST for Genomic Sequence Annotation

Jeremy Buhler Adapted by Wilson Leung Last Update 08232022 Overview What is comparative annotation How to measure similarity between biosequences How to decide whether two sequences are similar enough. tracking, including browsing of an annotation's edit history and full undo/redo functions. Real. -time updating: edits in one client are instantly pushed to all other clients. Convenient . management of user login, authentication, and edit permissions. Drosophila. An introduction to web tools, databases and NCBI BLAST. Wilson Leung . 08/2016. Agenda. GEP annotation project overview. Web databases for . Drosophila. annotation. UCSC Genome Browser. 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. Xuhua Xia. xxia@uottawa.ca. http://dambe.bio.uottawa.ca. Why string matching?. Early applications: . Sequence similarity between an oncogene (genes in viruses that cause a cancer-like transformation of the infected cells), v-sis, and the platelet-derived growth factor (PDGF). . Jundi. Wang. School of Computing. CSC691. 09/08/2013. 2. Overview. 1.Introduction of BLAST . Background of BLAST. Programs in BLAST. Function of BLAST. 2.Application of BLAST. Chris Shaffer July 2012. Last update: 08/2018. Annotation . “Big Picture” of annotation and then one practical example. This technique may not be the best with other projects (e.g. corn, bacteria). 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 . 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. Last Updated: 12/26/2021. Wilson Leung and Chris Shaffer. Agenda. Overview of the GEP annotation project. GEP annotation strategy. Types of evidence. Analysis tools. Web databases. Annotation of a single isoform (walkthrough). 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. 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 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.