GENOMICS AND BIOINFORMATICS LAB.

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GENOMICS AND BIOINFORMATICS LABName ______________________5 pointsLab __________________________Part 2: BioinformaticsIn this activity you will learn how to use various programs on the internet that allow you to search for and manipulateDNA and protein sequence data. Many of the programs are available through government run websites such as theNational Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI).BLASTA BLAST search is a way to identify protein or DNA sequences related to the one you are interested in. BLASTstands forBasicLocalAlignmentSearchTool. The emphasis of this tool is to find regions of sequence similarity,which will yield functional and evolutionary clues about the structure and function of your novel sequence. A blastwebsite can be found at:http://blast.ncbi.nlm.nih.gov/Blast.cgiAt this website you will want to use either “nucleotide blast” or “protein blast”.How to “BLAST”:Click “nucleotide blast” or “protein blast” depending on type of sequence. Copysequence (either DNA or amino acid), and paste it within box on webpage. Under thedatabasepull-downmenu, select “nucleotide collection” for nucleotide or “non-redundant protein sequence” for proteins. Next,click on “Blast” at bottom of page. Results will appear in several seconds. Scroll down to see matches.Click on a match to get more details.Restriction Digest AnalysisThere are several programs that search a DNA sequence for known restriction sites – very useful when trying toclone a gene. A nice complete site is:http://tools.neb.com/NEBcutter2/index.phpHow to “digest” a DNA sequence:Copy and paste a nucleotide sequence into the box on the webpage.Click “submit” on the right side. You will then see a map of your sequence with many different restrictionsites. You can click on the lower right tab “0 cutters” or “1 cutters” to see which enzymes do not digest thesequence and which ones digest it only once.Nucleotide TranslationTranslating a DNA sequence into an amino acid sequence can be time consuming. Fortunately there are programsavailable that can do it in a blink of an eye. This website provides a good program for translating DNA sequence:http://www.ebi.ac.uk/Tools/emboss/transeq/How to “translate”:Copy and paste DNA sequence into box on website. Click “Run” at lower right. In afew seconds the amino acid sequence will appear (using the single letter name for amino acids).Sequence AlignmentThese programs allow you to align two or more nucleotide or protein sequences. One easy to use site is:http://www.ebi.ac.uk/Tools/emboss/align/Once here, click on thenucleotide linknext to Needle (EMBOSS) if you are aligning nucleotide sequences,or theprotein linkif you are aligning protein sequence.How to “align” two sequences:All you have to do is copy and paste each sequence into the boxes and hit“Submit”
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