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Tut3 2022

The document provides instructions for writing programs to analyze DNA sequences, including: 1) Calculating AT content and complementing a DNA sequence. 2) Finding restriction fragments after digestion with EcoRI. 3) Separating coding and non-coding regions and calculating the percentage that is coding. 4) Splitting a genomic sequence into coding and non-coding parts and writing them to separate files. 5) Creating a FASTA file with 3 sequences in uppercase only containing bases A, T, G and C.

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Jia Lin
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15 views4 pages

Tut3 2022

The document provides instructions for writing programs to analyze DNA sequences, including: 1) Calculating AT content and complementing a DNA sequence. 2) Finding restriction fragments after digestion with EcoRI. 3) Separating coding and non-coding regions and calculating the percentage that is coding. 4) Splitting a genomic sequence into coding and non-coding parts and writing them to separate files. 5) Creating a FASTA file with 3 sequences in uppercase only containing bases A, T, G and C.

Uploaded by

Jia Lin
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as DOCX, PDF, TXT or read online on Scribd
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1) Calculating AT content

Write a program that will print out the AT content of this DNA sequence.

DNA sequence: ACTGATCGATTACGTATAGTATTTGCTATCATACATATATATCGATGCGTTCAT

The sample outcome is :

AT content is 0.6851851851851852

2) Complementing DNA

Write a program that will print the complement of this sequence.

DNA sequence: ACTGATCGATTACGTATAGTATTTGCTATCATACATATATATCGATGCGTTCAT

Sample output:

TGACTAGCTAATGCATATCATAAACGATAGTATGTATATATAGCTACGCAAGTA

The final outcome

tCTGtTCGtTTtCGTtTtGTtTTTGCTtTCtTtCtTtTtTtTCGtTGCGTTCtT

tCaGtaCGtaatCGatatGataaaGCataCtatCtatatataCGtaGCGaaCta

tgaGtagGtaatgGatatGataaaGgatagtatgtatatatagGtaGgGaagta

tgactagctaatgcatatcataaacgatagtatgtatatatagctacgcaagta

TGACTAGCTAATGCATATCATAAACGATAGTATGTATATATAGCTACGCAAGTA
3) Restriction fragment lengths

The sequence contains a recognition site for the EcoRI restriction enzyme, which cuts at the motif
G*AATTC (the position of the cut is indicated by an asterisk). Write a program that will calculate the size
of the two fragments that will be produced when the DNA sequence is digested with EcoRI.

DNA sequence: ACTGATCGATTACGTATAGTAGAATTCTATCATACATATATATCGATGCGTTCAT

Sample output:

1. Assign variable: my_dna


2. Find GAATTC---- my_dna.find(“GAATTC”)
3. Calculate length -----frag1_len=my_dna.find(“GAATTC”)+1
4. Calculate length of frag 2----- frag2_len=len(my_dna)-frag1_len

4) Splicing out introns,

section of genomic DNA:


ATCGATCGATCGATCGACTGACTAGTCATAGCTATGCATGTAGCTACTCGATCGATCGA
TCGATCGATCGATCGATCGATCGATCATGCTATCATCGATCGATATCGATGCATCGACT ACTAT

It comprises two exons and an intron. The first exon runs from the start of the sequence to the sixty-
third character, and the second exon runs from the ninetyfirst character to the end of the sequence.

a) Write a program that will print just the coding regions of the DNA sequence.
Sample output:

b) Using the data from a, write a program that will calculate what percentage of the DNA sequence
is coding.

Sample output:
78….
c) Write a program that will print out the original genomic DNA sequence with coding bases in
uppercase and non-coding bases in lowercase.

Sample outcome:

Exo1=my_dna[0:63]

Exo2=my_dna[90:]

Noncoding=my_dna[63:90]

Exon1+non_coding.lower（）+exon2

4. Splitting genomic DNA

Write a program that will split the genomic DNA from file genomic_dna.txt into coding and non-coding
parts, and write these sequences to two separate files.

5. Write a program that will create a FASTA file (output.txt) for the following three sequences – make
sure that all sequences are in uppercase and only contain the bases A, T, G and C.

Sequence
DNA sequence
header

ABC123 ATCGTACGATCGATCGATCGCTAGACGTATCG

DEF456 actgatcgacgatcgatcgatcacgact

HIJ789 ACTGAC-ACTGT--ACTGTA----CATGTG
Sample outcome

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