2. Dr. Kim at Ewha Research Center performed shotgun Sanger sequencing on ar unknown DNA sample, and obtained the following reads (12 reads). Since the length of each read is quite short, Dr. Kim ran the original sample in a gel electrophoresis, and realized tha the original DNA is just 50 base pairs long. (Please note that the resolution of ge electrophoresis is not so good. Thus, we cannot figure out the exact length of DNA using ge electrophoresis in the real world.) 1) САСТС ССАGT GTACC T 3) GGAGT CAАТC GC 5) GGCTG TGCTT GG 7) GATGG CTGTG 9) CAGTG TACCT GCA 11) TGCAA GCCGA G 2) AGCCG AGATG GCTG 4) CTGCA AGCCG A 6) CTTGG AGTCA ATCGC 8) САСТС ССAG 10) GCTGT GCТTG G 12) TGCTT GGAGT (a) Find the sequence of the original DNA (reconstruction), and align each read with the reconstructed DNA sequence. (hint: put all reads on a ppt slide, and move them around to find overlaps.) (b) Calculate coverage at each nucleotide position of the reconstructed DNA, i.e., hov many reads cover that particular nucleotide.
2. Dr. Kim at Ewha Research Center performed shotgun Sanger sequencing on ar unknown DNA sample, and obtained the following reads (12 reads). Since the length of each read is quite short, Dr. Kim ran the original sample in a gel electrophoresis, and realized tha the original DNA is just 50 base pairs long. (Please note that the resolution of ge electrophoresis is not so good. Thus, we cannot figure out the exact length of DNA using ge electrophoresis in the real world.) 1) САСТС ССАGT GTACC T 3) GGAGT CAАТC GC 5) GGCTG TGCTT GG 7) GATGG CTGTG 9) CAGTG TACCT GCA 11) TGCAA GCCGA G 2) AGCCG AGATG GCTG 4) CTGCA AGCCG A 6) CTTGG AGTCA ATCGC 8) САСТС ССAG 10) GCTGT GCТTG G 12) TGCTT GGAGT (a) Find the sequence of the original DNA (reconstruction), and align each read with the reconstructed DNA sequence. (hint: put all reads on a ppt slide, and move them around to find overlaps.) (b) Calculate coverage at each nucleotide position of the reconstructed DNA, i.e., hov many reads cover that particular nucleotide.
Human Anatomy & Physiology (11th Edition)
11th Edition
ISBN:9780134580999
Author:Elaine N. Marieb, Katja N. Hoehn
Publisher:Elaine N. Marieb, Katja N. Hoehn
Chapter1: The Human Body: An Orientation
Section: Chapter Questions
Problem 1RQ: The correct sequence of levels forming the structural hierarchy is A. (a) organ, organ system,...
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Transcribed Image Text:2.
Dr. Kim at Ewha Research Center performed shotgun Sanger sequencing on
an
unknown DNA sample, and obtained the following reads (12 reads). Since the length of each
read is quite short, Dr. Kim ran the original sample in a gel electrophoresis, and realized that
the original DNA is just 50 base pairs long. (Please note that the resolution of gel
electrophoresis is not so good. Thus, we cannot figure out the exact length of DNA using gel
electrophoresis in the real world.)
1) САСТС ССAGT GTACC T
3) GGAGT CAАТC GC
5) GGCTG TGCTT GG
7) GATGG CTGTG
9) CAGTG TAССT GCA
11) TGCAA GCCGA G
2) AGCCG AGATG GCTG
4) CTGCA AGCCG A
6) CTTGG AGTCA ATCGC
8) САСТС ССAG
10) GCTGT GСТTG G
12) TGCTT GGAGT
(a)
Find the sequence of the original DNA (reconstruction), and align each read with
the reconstructed DNA sequence. (hint: put all reads on a ppt slide, and move them around
to find overlaps.)
(b)
Calculate coverage at each nucleotide position of the reconstructed DNA, i.e., how
many reads cover that particular nucleotide.
R×N
(c)
The average coverage of the sequencing is defined as
where R is the
average length of reads, N is the number of reads, and L is the length of the whole genome.
Using this definition, find the average coverage of this shotgun Sanger sequencing.
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