1. Aligning Grass Protein Sequences Using PAM-Modified Global Alignment
Yifei Zhang
May 7, 2018

2. Utilizing the PAM250 Matrix
Obtain the table
Build a dictionary
Modify the globalAlign Function

3. Gramineae, or the grasses family
Evolutionary History of the Grasses
Elizabeth A. Kellogg
Plant Physiology Mar 2001, 125 (3)  ; DOI:  /pp  
Indica rice: long-grained,
Harder after cooked
Japonica rice: short-grained,
Softer after cooked

4. Three proteins analyzed:
Granule-bound starch synthase, which is related to the stickiness of the seed after cooked
GS3 protein/seed length and weight protein, regulates grain size.
 Betaine aldehyde dehydrogenase/badh2/fragrance protein. An allele located on the gene is a major factor associated with aroma.  

5. Finding and processing data
Sample : Betaine aldehyde dehydrogenase [Zea mays L.]
NCBI Reference Sequence: NP_
506
mmasqamvplrqlfvdgewrppaqgrrlpvvnptteahigeipagtaedvdaavaaaraa
lkrnrgrdwarapgavrakylraiaakvierkqelaklealdcgkpydeaawdmddvagc
feyfadqaealdkrqnspvslpmetfkchlrrepigvvglitpwnypllmatwkvapala
agcaavlkpselasvtcleladickevglppgvlnivtglgpdagaplsahpdvdkvaft
gsfetgkkimaaaapmvkpvtlelggkspivvfddvdidkavewtlfgcfwtngqicsat
srllvhtkiakefnekmvawaknikvsdpleegcrlgpvvsegqyekikkfilnaksega
tiltggvrpahlekgffieptiitdittsmeiwreevfgpvlcvkefstedeaielandt
qyglagavisgdrercqrlseeidagiiwvncsqpcfcqapwggnkrsgfgrelgeggid
nylsvkqvteyisdepwgwyrspskl
Remove spaces and number:
def clean(s1): result = ''.join(i for i in s1 if not i.isdigit())
result = result.split()
result = ''.join(result
return result

6. Modify Global alignment
Define getPam function that builds a dictionary from the PAM 250 text table(white space eliminated) Ex. int(pam[string1[a-1]][string2[b-1]]) replaces match
Same procedure as HW6.2
Initialize table and backtrack
Fill in scores and directions
From backtrack start reverse alignment
Reverse sequence to get alignment
Modify Global alignment

7. Results A= Zea mays L. B= Oryza sativa indica group
C= Oryza sativa japonica group
1= granule- bound starch synthase-stickiness
2=GS3-grain size
3=badh2-fragrance
Scores for the second and third sequences are always higher than either one of them scoring with the first sequence :
Two Oryza sativa cultivars are more closely related (As expected)
Average indels for pair 1&2: 5
Average indels for pair 4&5: 》〉》〉》〉》 GS3 as the most different protein in the three
Average indels for pair 7&8: 3

8. What comes after
Analyze more species from the grass family and construct a simple phylogenetic tree using alignment results
Dig into different proteins and find out more about the similarities across species.
 Develop a simple version of BLAST for protein alignment, (applying it to multiple pairs of sequences at the same time).

9. End
Thank you.