LESSON 4 Using Bioinformatics to Analyze Protein Sequences

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LESSON 4CLASS SET6. The next screen will show you a graphicalillustration of every open reading frame foundin your DNA sequence, highlighted as a solidturquoise bar (shown next to the black arrowbelow in Figure 2).7. Above this illustration, there is a drop-down menunext to the Redraw button (shown inside theblack circle in Figure 2) that allows the scientist toselect the minimum protein length displayed:50 amino acids, 100 amino acids, or 300 aminoacids. [Note: The average protein length ineukaryotes is about 300 amino acids.] If it is notalready set at 100, select 100 from the drop-downmenu and click Redraw. See Figure 2.8. To the right of this illustration, ORF Finder listswhich reading frames contain potential proteinsof greater than 100 amino acids, and the basepositions of each reading frame (shown insidethe black square in Figure 2).Figure 1: ORF Finder. Source: NCBI ORF Finder.9. How many open reading frames contain potential proteins greater than 100 amino acids long?10. Which open reading frame contains the longest potential protein?11. What are the base positions of this potential protein?(A) From base #:___________(B) To base #:__________12. What is the length of this potential reading frame (in nucleotides)?Using Bioinformatics: Genetic ResearchCodon: Series of three nucleotidesin a row that specifies the geneticcode information for a particularamino acid when translating agene into protein. For example,the codon CCG codes for theamino acid proline (P). Also called anucleotide triplet.Nucleotide triplets: Series of threenucleotides in a row, usually called a“codon,” that specifies the geneticcode information for a particularamino acid when translating agene into protein. For example, thenucleotide triplet or codon CCGcodes for the amino acid proline (P).Figure 2: Redrawing the Minimum Protein Length. Source: NCBI ORF Finder.146©Northwest Association for Biomedical Research—Updated October 2012
LESSON 4CLASS SET13. Click on the graph where you seethe longest reading frame. You shouldsee the DNA sequence and translatedprotein appear below the ORF Finderdisplay, as shown in Figure 3.14. How long is this protein (i.e., howmany amino acids)?15. Is the length of the protein similarto what you would expect given thelength of the DNA sequence in Step#13 above? Why or why not? [Note:Remember that each codon for oneamino acid is three nucleotides long.]Figure 3: Choosing the Protein with the Longest Open Reading Frame.Source: NCBI ORF Finder.PART II: Multiple Sequence Alignments Using Protein SequencesNow that you have the protein sequence translated from your barcode DNA, what can you do with it? Many geneticresearchers compare protein sequences from different species by performing multiple sequence alignments, similarto those you made with your DNA sequences in the previous lesson. This makes it possible to identify amino acidchanges among species, which can lend insight into the functional consequences of protein evolution.16. Go to the Bio-ITEST website and click on theResources tab (gray box, Figure 4): http://www.nwabr.org/curriculum/advanced-bioinformaticsgenetic-research.17. Click on the Protein sequences file for your group(black box, Figure 4).18. Copy all of your group’s protein sequences,including the species name and the caret “>.” Eachof these sequences contains the same open readingframe that you identified with ORF Finder in Part I. Besure to select and copy all of the sequences.19. Go to ClustalW2 at the European BioinformaticsInstitute (EBI) at: http://www.ebi.ac.uk/Tools/msa/clustalw2/.20. Paste your Group Protein sequences into thesequence box in STEP 1 (black arrow, Figure 5).21. Select Protein from the drop down menu (blackbox, Figure 5).22. Click Submit (gray arrow, Figure 5).Figure 4: Obtain Your Group Protein Sequences from the Bio-ITESTResources Page for Advanced Bioinformatics. Source: NWABR.Lesson 4 – Using Bioinformatics to Analyze Protein Sequences147©Northwest Association for Biomedical Research—Updated October 2012
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LESSON 4 Using Bioinformatics to Analyze Protein Sequences

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