1. Sequence Alignments—part 2
Week 4

2. Independent Project Gene Due 9/25 (Monday) must be submitted by email
Quiz 1: 10/9
~35 questions theory and practical (questions based on the programs and websites we have used). Paper quiz, no computer work.

3. Review for quiz

4. Review for quiz

5. Review for quiz

6. Review for quiz

7. Review for quiz

8. Review for quiz

9. Learning Objectives:
Learn to use Online Mendelian Inheritance in Man (OMIM)
Understand the different types of mutations and how they can alter protein products
Use EMBOSS-Needle to generate a pairwise alignment
Determine if mutations fall within coding sequences or in untranslated regions (UTR)

10. Identifying mutations in genes of interest
DNA
RNA
protein
phenotype
Bioinformatics and Functional Genomics, 2nd Edition. (2014).

12. A genetic map of Human Chromosome 7
Location of the gene responsible for Cystic Fibrosis in 90% of people of Northern European descent

13. Sequence of the Cystic Fibrosis Gene: CFTR

14. The deletion of these three base pairs is responsible

15. DNA uses a triplet code to specify amino acids
DNA sequence:
GGGAGTGTAGATCGT
GGG AGT GTA GAT CGT
Gly—Ser—Val—Asp—Arg
Codons:
Amino acids: 15

16. Mutation resulting in a single base pair substitution
GGG AGT GTA GAT CGT
GGG AGT GCA GAT CGT
Original Sequence
Base substitution
Result is an amino acid substitution Val>Ala 16

17. GTA codes for Val (V) while GCA codes for Ala (A)
Korf, Y., Yandell, M. & Bedell, J. BLAST: an essential Guide to the Basic Local Alignment Search Tool (Sebastopol; O’Reilly, 2003).

18. Single Base Substitutions
Neutral: No amino acid change
Missense: Amino acid substitution (change)
Nonsense: Changes codon to a termination sequence (leads to a truncated protein) (stop) 18

19. An example of a neutral change: GTA>GTG
Korf, Y., Yandell, M. & Bedell, J. BLAST: an essential Guide to the Basic Local Alignment Search Tool (Sebastopol; O’Reilly, 2003).

20. Single Base Substitutions
Neutral: No amino acid change
Missense: Amino acid substitution (change)
Nonsense: Changes codon to a termination sequence (leads to a truncated protein) (stop) 20

21. GTA codes for Val (V) while GCA codes for Ala (A)

22. Single Base Substitutions
Neutral: No amino acid change
Missense: Amino acid substitution (change)
Nonsense: Changes codon to a termination sequence (leads to a truncated protein) (stop) 22

23. Mutations that results in a TER/stop codon
Korf, Y., Yandell, M. & Bedell, J. BLAST: an essential Guide to the Basic Local Alignment Search Tool (Sebastopol; O’Reilly, 2003).

24. Mutation resulting in a single base pair deletion
Original Sequence
GGG AGT GTA GAT CGT
GGG AGT GAG ATC GT
Base Deletion
Result is an alteration in many codons 24

25. Mutation resulting in a single base pair deletion
Original Sequence
GGG AGT GTA GAT CGT
Gly—Ser—Val—Asp—Arg
Gly—Ser—Glu—Ile— ?
GGG AGT GAG ATC GT?
Base Deletion
Result is an alteration in many codons 25

26. Mutation resulting in a single base pair insertion
Original Sequence
GGG AGT GTA GAT CGT
GGG AGT GCT AGA TCG T
Base Deletion
Result is an alteration in many codons 26

27. Mutation resulting in a single base pair insertion
Original Sequence
GGG AGT GTA GAT CGT
GGG AGT GCT AGA TCG T
Gly—Ser—Val—Asp—Arg
Gly—Ser—Ala—Arg—Ser
Base Deletion
Result is an alteration in many codons 27

28. Insertions and Deletions are often referred to as InDels
GGG AGT GTA GAT CGT
GGG AGT GTT AGA TCG T
Sequence 1
Sequence 2 28

29. Insertions and Deletions are often referred to as InDels
GGG AGT GTA GAT CGT
GGG AGT GTT AGA TCG T
Sequence 1
Sequence 2
Is it an insertion in sequence 2 or a deletion in sequence 1? 29

30. Insertions and deletions can affect large regions of sequence
Entire chromosomes can be deleted (lost) 30

31. Duplications are a specialized type of insertion
Genes
Repeats
Location 31

32. Trinucleotide Repeats are examples of duplications
~30 genetic diseases in humans are due to expansion of simple repeats.
Genes
Repeats
Location 32

33. Where to find OMIM?

34. How to use OMIM

35. How to use OMIM

36. OMIM links genotype to phenotype

37. OMIM catalogues disorders/diseases

38. Allelic variants describe mutations in genes

39. Table view gives a summary of variants

40. How to use OMIM

41. How to use OMIM
GLY12SER: Glycine at position12 substituted with Serine
3-BP INS, GLY11INS: 3-base pair insertion, Glycine inserted at position 11

42. How to use OMIM
GLY12SER: Glycine at position12 substituted with Serine
3-BP INS, GLY11INS: 3-base pair insertion, Glycine inserted at position 11

43. How to use OMIM

44. Common abbreviations in OMIM
DEL: Deletion
INS: Insertion
DUP: Duplication
TER: Terminator/Stop Codon
Amino acids are abbreviated using 3 letter code: PRO: Proline
Nucleotides are abbreviated using 1 letter code: A,G,T and C
NT: Nucleotide (usually referring to position i.e. NT305)
BP: Base pair (3BP INS: three base pair insertion)
KB: Kilo Base (1000 Bases)
IVS: Intervening sequence (intron) (sometimes noted as +1 or -1)

45. Generate a pairwise sequence comparison

46. Paste FASTA formatted text files

49. Pairwise alignment allows you to identify mutations

50. Pairwise alignment allows you to identify mutations
2 BP DEL at NT position 44
Substitution G to A at NT position 152

51. Exons are numbered by their location
Lodish, H. et al. Molecular Cell Biology (New York; W.H. Freeman, 2000). 52

52. Exons include 5’UTR, coding sequence and 3’UTR
Exon 1 includes 5’UTR and coding sequence
Exon 3 includes 3’UTR and coding sequence
Lodish, H. et al. Molecular Cell Biology (New York; W.H. Freeman, 2000). 53

53. Worksheet