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

2. 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 Identifying Genes 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. 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 BLAST Databases 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. 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# Comparing Sequences