Description
UMUC BIOT630
Lecture 3 Exercise – “Due Version”
Question 1.
Align the following two fictional sequences using the Dot Matrix Method.
Use “X” to denote a dot.
P E A N U T T Y B U T T E R Y A N D J E L L Y I S H
P
E
A
N
U
T
B
U
T
T
E
R
A
N
D
J
E
L
L
Y
Question 2.
What is the sequence alignment for the aligned sequences in question 1?
Answer = ?
Question 3a.
What is the RefSeq protein sequence (NP_075249.1) for Rat (Rattus norvegicus) AQP9?
Answer = ?
Question 3b.
What is the RefSeq protein sequence (NP_001192762.2) for Cow (Bos taurus) AQP9?
Answer = ?
Question 3c.
Using DotletJS (https://dotlet.vital-it.ch), show what regions between the protein
sequence you provided for your answer to Q3a (=Rat AQP9) and the protein sequence
you provided for your answer to Q3b (= Cow AQP9) are the high scoring (i.e., highly
related) regions. Note, these would be the regions that occur along the diagonal.
Answer = ?
Question 4.
Why was the BLOSUM type matrix used in question 3 for comparing rat and cow? Expected
answer involves discussion on whether the species from which the sequences were compared
are distant vs closely related. Specific matrix number is not required as part of your
answer. Rather, only the matrix family type and why. Revisit the Lecture Slides if confused how
to answer this question.
Answer = ?
Question 5.
What general type of substitution matrix would be best to use by design if you were comparing
AQP9 protein sequences between rat and mouse? Expected answer involves discussion on
whether rat and mouse are distant vs closely related and what substitution matrix type would be
best suited based on the relatedness. Specific matrix number is not required as part
of your answer. Rather, only the matrix family type and why. Revisit the Lecture Slides if
confused how to answer this question.
Answer = ?
ttttttttUMUC BIOT630 ttttttt
Lecture 3 Exercise – “Practice Version”
Question 1.
Align the following two fictional sequences using the Dot Matrix Method.
Use “X” to denote a dot.
H
H
O
T
T
D
O
G
G
K
E
T
C
H
U
P
Y
A
N
D
M
U
S
T
A
R
D
D
Y
O
T
D
O
G
K
E
T
C
X
H
U
P
A
N
D
M
U
S
T
A
R
D
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Question 2.
What is the sequence alignment for the aligned sequences in question 1?
Answer =
H O T – D O G – K E T C H U P – A N D M U S T A R D
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H O T T D O G G K E T C H U P Y A N D M U S T A R D D Y
Question 3a.
What is the RefSeq protein sequence (NP_062031.1) for Rat (Rattus norvegicus) AQP8?
Answer = https://www.ncbi.nlm.nih.gov/protein/NP_062031.1?report=fasta =
>NP_062031.1 aquaporin-8 [Rattus norvegicus]
MSGEQTPMCSMDLREIKGKETNMADSYHGMSWYEQYIQPCVVELLGSALFIFIGCLSVIENSPNTGLLQP
ALAHGLALGLIIATLGNISGGHFNPAVSLAVTLVGGLKTMLLIPYWVSQLFGGMIGAALAKVVSPEERFW
NASGAAFAIVQEQEQVAEALGVEIVMTMLLVLAVCMGAVNEKTMGPLAPFSIGFSVIVDILAGGGISGAC
MNPARAFGPAVMAGYWDFHWIYWLGPLLAGLFVGLLIRLFIGDEKTRLILKSR
Question 3b.
What is the RefSeq protein sequence (NP_001193536.1) for Cow (Bos taurus) AQP8?
Answer = https://www.ncbi.nlm.nih.gov/protein/NP_001193536.1?report=fasta =
>NP_001193536.1 aquaporin-8 [Bos taurus]
MFTEAAVSMCDLESGSVKVKEPSNRGRWHGCWYERLVQPCLVELLGSALFIFIGCLSVIENGPDTGRLQP
ALAHGLALGLVIATLGNISGGHFNPAVSLAAMLVGGLKLTMLFPYWISQLCGGLIGATLAKAVSPEDRFW
NATGAAFVTVQESEQVAGAVVAEVILTTLLVLTVCTGAINEKTLGPLAPFCIGFSVTVDILAGGAVSGAC
MNPARAFGPAMVANHWDYHWIYWLGPLLASLLVGVLIRFFIGDAKIRLILKGR
Question 3c.
Using DotletJS (https://dotlet.vital-it.ch), show what regions between the protein
sequence you provided for your answer to Q3a (=Rat AQP8) and the protein sequence
you provided for your answer to Q3b (= Cow AQP8) are the high scoring (i.e., highly
related) regions. Note, these would be the regions that occur along the diagonal.
To answer, enter in the Rat sequence as “SEQUENCE 1 then click “Save Sequence”:
Then, enter in the Cow sequence as “SEQUENCE 2” then click “Save Sequence”:
Next, click on the radio button “SAVED SEQUENCES”:
… and make sure the Rat sequence is “SEQEUNCE 1” by selecting “Sequence 1”:
… and that the Cow sequence is “SEQUENCE 2” by selecting “Sequence 2”:
You should then see in the Dotlet representation both your sequences selected:
Next, adjust the top slider so that it is positioned where the tail of the larger blue
distribution ends:
As you do, your Dotlet representation will dynamically update:
Copy/paste screen shot of this result image as your answer.
Purchase answer to see full
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