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Genomics and Bioinformatics Lab
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Added on 2019-09-20
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This lab activity teaches how to use various programs on the internet that allow you to search for and manipulate DNA and protein sequence data. It covers BLAST, Restriction Digest Analysis, Nucleotide Translation, and Sequence Alignment. The lab also provides two unknown nucleotide sequences to perform the above-mentioned techniques and answer questions based on the results.
Genomics and Bioinformatics Lab
Added on 2019-09-20
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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 the National 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. BLAST stands for Basic Local Alignment Search Tool. 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 blast website 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. Copy sequence (either DNA or amino acid), and paste it within box on webpage. Under the database pull-down menu, 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 to clone 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 restriction sites. You can click on the lower right tab “0 cutters” or “1 cutters” to see which enzymes do not digest the sequence and which ones digest it only once.Nucleotide TranslationTranslating a DNA sequence into an amino acid sequence can be time consuming. Fortunately there are programs available 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 a few 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 the nucleotide link next to Needle (EMBOSS) if you are aligning nucleotide sequences,or the protein link if 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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