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BLAST: Basic Local Alignment Search Tool

BLAST: Basic Local Alignment Search Tool. BLAST is a software used to analyze genetic information. It can identify existing genes and predict novel ones. Robert (R.J.) Sperazza. The data is collected and stored in huge databases.

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BLAST: Basic Local Alignment Search Tool

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  1. BLAST: Basic Local Alignment Search Tool • BLAST is a software used to analyze genetic information • It can identify existing genes andpredict novel ones Robert (R.J.) Sperazza • The data is collected and stored in huge databases • The information can be used to compare homology in different organisms

  2. Identifying Genes • Various programs exist to identify genes • Classification method depends on source of info • Nucleotides and/or proteins are the inputs • Nucleotides can also be translated and compared to protein sequences or other translated nucleotides • Look for certain characteristic sequences to identify the gene Description of the various BLAST programs. Each uses different starting materials and reference sequences. Figure from http://blast.ncbi.nlm.nih.gov/Blast.cgi

  3. BLAST Databases • Each has its own criteria for recognizing genes • Each has own strengths/weaknesses • Major examples of websites: • UCSC Genome Browser • FlyBase • Gene Record Finder • NCBI Example of an input screen for a BLAST run. User can select the database and query (Program), and the source of the sequence file (or manually insert the sequence). Figure from flybase.org

  4. Comparing Sequences • Testing for homology allows comparison of organisms • Example: look for the presence of certain genes in similar fruit fly species • Find % of similarity to gauge how evolutionarily conserved the sequence is • http://www.brainrush.com/cards/edit/topics-in-biomedicine-ch-1#

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