Question

Question 4 Part A [10 marks] A human genome has been re-sequenced using a sequencing technology that produces 100 bp reads of high quality data. The DNA was sheared to make a paired-end library with a size range of 1500 bp +- 500 bp and sequenced to generate paired-end reads. The analysis pipeline takes short-read sequence data and aligns it to a repeat-masked version of the reference human genome sequence assembly using BLASTN. This table summarizes the results from three pairs of reads Mate Sequence Pain Strand End Chromosome Start Stop Forward5 Reverse 5 Forward 21 Reverse 21 63.951 65,391 64,050 65,290 12,233,184 |12,233,285+ 12,234,670 12,234,581- 41,986,536 41,986,637+ 41,099,12441,099,223+ 1 4 Forward 12 Reverse 12 i.Interpret these results. Include a simple diagram. [5 marks] ii. If these six sequences were single-end reads rather than paired-end reads, would they have been as informative? Explain why. [5 marks]

Answer 1

1) i-                (start)    63,951 Anti-sense strand(-) forward $\rightarrow$ 64050 (stop                        

2)                   (start)    65,290             sense strand(+) reverese   $\leftarrow$                            (stop) 65,391            

3)                    (start) 12.233,184           sense strand(+) reverse $\leftarrow$ ( stop) 12,233,285

4)    (start) 12,234,670 Antisense strand(-)    forward   $\rightarrow$    (stop) 12,234,581

5.)    (start)    41,986,536    sense strand(+) reverse $\leftarrow$    ( stop) 41,986,63

6.) ( start)       41,099.124    sense strand(+) reverse $\leftarrow$    (stop)41,099.22

The above diagram   is a simple representation of DNA strand and out of six samples,two are antisense running in the forward direction and rest four and sense strand running in the reverse direction.The start and stop coding nucleotide base sequences are mentioned.

ii)No, they would not be soo informative.Paired ends provide data about nucleotide base pairing,amino acid sequence and

hence protein coded by them.Entire genome sequencing would be easy in case of double paired ends then single paired ends.