How to do questions like this? Could you explain? Question 4 Part A quick alignm

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How to do questions like this? Could you explain? Question 4 Part A quick alignment of all the words, or k-mers, of BLAST and other programs create an index In this problem, size k in the query and target sequences, and look up matches in that index. table. There is you will need to align the 10bp query to the 15bp target by filling in the k-mer no scoring scheme here and you can assume that a mismatch or two is permissible. Target sequence: base f 123456789012345 Query sequence: base 1234567890 ATCGGAATCA. i. Carefully draw the following table in your answer book and fill in the k-mer word locations and frequencies. All relevant k-mers are shown and sorted in all marks] Start locations of word in WORD TARGET CUERY ATT GGA LAC ii. Write the target and query sequences in your answer book and underline the 3-mer matches in the sequences. [2 marks] iii. If you can connect any pairs of matches to extend a match, show the alignment and extension. 13 marks] iv. Write out the alignment for any matches that could be extended. 12 marks] Page 6 of 7

Explanation / Answer

i.

Start locations of word in

WORD

TARGET

QUERY

AAT

6

ACG

3

ATC

8

1,7

ATT

11

CAT

10

CGG

4

3

CTA

1

GAA

5

GAT

7

GGA

6

4

GGG

5

TAC

2

TCA

9

8

TCA

9

8

TCG

2

TGC

13

TTG

12

II. 3-mer matches in the sequences are: ATC, CGG, GGA and TCA.

III. ATC and TCA are matching. The extended match is ATCA (Location of target sequence is 8 and location of Query sequence is 7)

iv. ATC can be extended to ATCA.

Start locations of word in

WORD

TARGET

QUERY

AAT

6

ACG

3

ATC

8

1,7

ATT

11

CAT

10

CGG

4

3

CTA

1

GAA

5

GAT

7

GGA

6

4

GGG

5

TAC

2

TCA

9

8

TCA

9

8

TCG

2

TGC

13

TTG

12

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