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Target: Intro. Bio. students (major/non-majors)

Using Hemoglobin to Introduce Bioinformatics Tools to General Biology Students Nancy Boury , Cristina Caldari-Farren, Scott Chirhart , Chrystal Ho Pao , Crystal Simien. Target: Intro. Bio. students (major/non-majors) Upon completion of this activity students should be able to:

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Target: Intro. Bio. students (major/non-majors)

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  1. Using Hemoglobin to Introduce Bioinformatics Tools to General Biology StudentsNancy Boury, Cristina Caldari-Farren, Scott Chirhart, Chrystal Ho Pao, Crystal Simien

  2. Target: Intro. Bio. students (major/non-majors) • Upon completion of this activity students should be able to: • Use basic Bioinformatics tools

  3. DNARNAProtein Synthesis Intro to Genomics How many genomes? How many genes per genome? How do you navigate in this sea of data? NCBI Ex. Pick a protein that you talked about? Hemoglobin Why?

  4. Why Hemoglobin? • Has been introduced in General Biology • Known diseases associated with it • Typically used as example of deleterious effects of point mutations • Duplications within the human genome • Adult, fetal, myoglobin • Well conserved

  5. How do we decide if two organisms are similar? Simple sequences DID YOU SEE THE CAT RUN DID YOU SEA THE CAT RUN DID YOO SEE TEE BAT RUT BAD OOO EEE TTT DOG SIT How are differences in similarity quantified? Intro to BLAST and how it works? Ex. Hemoglobin--Human vs. Asian Water Buffalo

  6. How do we decide if two organisms are similar? • Alignment • Gaps-2 • (HH) MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLL • (AWB)M - -LTAEEKAAVTAFWGKVHVDEVGGEALGRLL

  7. Substitution Matrices

  8. E-value • E-values of 10-4 and lower might indicate a significant homology. • E-values between 10-4 and 10-2 should be checked (may not be homologous). • E-values between 10-2 and 1probably do not indicate a good homology

  9. How do we decide if two organisms are similar? Similarities between proteins in one species? Similarities between one protein in many species? How do we determine if evolutionarily linked? What questions could you ask with this data?

  10. Aligning the sequences using MUSCLE

  11. Another way of looking at this is by creating an HMM logo

  12. Use of CONSURF for Fetal Hemoglobin Alpha Subunit 3D Image

  13. We can look at evolutionary linkage with the use of phylogenetic trees based on sequence data

  14. What could we ask the students to do? • Differences in conserved vs. non-conserved proteins? • List of possible proteins: • Hexokinase • ATPase • NADH dehydrogenase • Cytochromes • Actin

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