PPT-Run BLAST in command line mode

Yanbin Yin Fall 2014 1 http wwwncbinlmnihgov booksNBK52640 2 Why you do need to run BLAST in command line terminal NCBIs server does not have a database that you want to search. Track your software investments and understand how your Embarcadero software is being used With the Embarcadero License Center ELC you can have centralized and simplified control over license administration It is one more way Embarcadero Technologie 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. 1914 and 1915, Wyndham Lewis, ed.. Percival Wyndham Lewis. 1882-1957. the men of 1914. unpopular. politics – questionable at best. artist, writer, thinker. The Enemy – and its pitfalls. Vorticism. 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.. et BLAST . avanc. é. J.. S. .. Bernardes. /H. . Richard. Mat. ériel. :. Bioinformatics and Functional Genomics. Jonathan Pevsner, . Wiley-Blackwell. ed.. Outline. Introduction. . Definition of . in Chemical Lab. Safety News Blog. (for additional information on refrigerator safety see the “Equipment: Refrigerators and Freezers” safety moment). Refrigerator Blast. A . refrigerator door blew off and hit an inner pane of a double-paned window in a chemical lab at the University of South Florida. , Green, Henricks, Jones, Kennedy, . Mawhinney. , . Peluso. , Reilly, Schwartz, Shapiro, . Yanushevsky. Blast Localization and Sensing Technology. Image Courtesy of: . Stanislav. . Klabik. MOTIVATION. 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. are what most people think of as rocket scientists. They research, design, and develop nearly anything that flies, such as airplanes, spacecraft, and of course rockets. . Blast Off . helps explore how different rocket designs change the ability of the rocket to go great distances. Follow the advice of the station helper to find out if a structure makes a difference and why so you can make the best rocket based on the distance it travels while maintaining a fairly straight path. 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). Healthy hydration - the average person drinks 5.2 beverages a day.. No empty calories and dead nutrition.. . . . . . . . The average cola has 22 grams . of sugar . per 8 oz. . 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. 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 Team2. 邱冠儒 黃. 尹. 柔 田. 耕. 豪 蕭. 逸. 嫻 謝朝茂 . 莊閔. 傑. 2014/05/12. 1. BLAST. Basic local alignment search tool. Enable to compare query sequence of amino-acid or protein or DNA to database .