Scribd
Upload
41 views3 pages

Bioinformatics HW1

Uploaded by

Youssef Mohamed
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
41 views3 pages

Bioinformatics HW1

Uploaded by

Youssef Mohamed
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
You are on page 1/ 3

Given that your ID ends in 8 (even), we will proceed with the instructions to extend the

sequence from 5' to 3' direction, replacing T by U to find the RNA sequence.

1. Original DNA Sequence

Copy code
ATGAGCATGTCGAAACATGATTCACCGATCATCATCAAATTACTAATGTGCTGGAACTATATGCTATT
TACGTGAGACAATGACCCACATTAACCGGCCAATGGGA

2. Modified DNA Sequence with a Subsequence of 12 Nucleotides


We'll insert a 12-nucleotide subsequence containing the start codon ATG. Let's add this
subsequence ATGCGGCTAGAC after the second "ATG" codon for simplicity.

Modified DNA Sequence:

Copy code
ATGAGCATGCGGCTAGACATGTCGAAACATGATTCACCGATCATCATCAAATTACTAATGTGCTGGA
ACTATATGCTATTTACGTGAGACAATGACCCACATTAACCGGCCAATGGGA

3. Find the RNA Sequence (5' to 3')


Since the sequence extends from 5' to 3' and it’s even, replace T with U to convert DNA
into RNA.

Corresponding RNA Sequence:

Copy code
AUGAGCAUGCGGCUAGAC-AUGUCGAAACAUGAUUCACCGAUCAUCAUCAA-
AUUACUAAUGUGCUGGAACUAUAUGCUAUUUACGUGAGACAAUGACCCACAUUAACCGGCCA
AUGGGA

4. Identify the Codons in the RNA


RNA is read in groups of three nucleotides (codons). Here are the first few codons:
 AUG = Methionine (Start)
 AGC = Serine
 AUG = Methionine
 CGG = Arginine
 CUA = Leucine
 GAC = Aspartic acid
 AUG = Methionine
 UCG = Serine
 AAA = Lysine
 CAU = Histidine

So, the RNA codons for the first part of the sequence are as follows (this is not
exhaustive, you can continue based on how much you want to analyze):
objectivec

Copy code
AUG AGC AUG CGG CUA GAC AUG UCG AAA CAU GAU UCA CCG AUC AUC AUC AAU UAC
UAA UGU GCU GGA ACU AUA...
5. Determine the Amino Acids Produced
Using a codon chart, we translate the RNA into amino acids. The first few are as follows:
 AUG = Methionine (M)
 AGC = Serine (S)
 AUG = Methionine (M)
 CGG = Arginine (R)
 CUA = Leucine (L)
 GAC = Aspartic acid (D)
 AUG = Methionine (M)
 UCG = Serine (S)

So, the protein sequence for the first portion of the RNA is:
mathematica

Copy code
M-S-M-R-L-D-M-S-K-H...
You can continue this process to identify the entire amino acid sequence.

6. Possible Proteins from the Given Sequence


 Since translation starts at the first AUG (Methionine) codon and ends at a stop
codon (UAA, UAG, UGA), one protein is formed based on the first AUG start codon.
 If you check for other potential AUG codons in the sequence, you may find other
possible proteins depending on the stop codons present.

7. Mutation Analysis
Original sequence: ATTCACCGATCATCATCAAATT
Mutated sequence: TATGCTATTTAAATGCCACAAT

Transcription and Translation Effect:


1. Original sequence transcription: Replace T with U for RNA sequence:
o Original RNA: AUUCACCGAUCAUCAUCAAAUU
2. Mutated sequence transcription:
o Mutated RNA: UAUGCUAUUUAAAUGCCACAAU
3. Amino Acid Translation:
o Original: Using the original sequence’s codons: AUU CAC CGA UCA UCA UCA
AAU U → Translates to I-H-R-S-S-S-N
o Mutated: Using the mutated sequence: UAU GCU AUU UAA AUG CCA CAA
U → Translates to Y-A-I-STOP

The mutated sequence introduces a STOP codon (UAA) much earlier, which means the
protein will be truncated and likely non-functional.

8. Longest Common Substring Between Two Sequences


Let's choose the following two sequences:
 Sequence 1: ATGCGTCAACATGCCGTCAT
 Sequence 2: GTCATGCCGTTACGTGAGAC
By comparing the two sequences, the longest common substring is:

Copy code
GTCATGCCG
This substring is common to both sequences, and its length is 9 nucleotides.

Summary:
 Modified RNA Sequence: AUGAGCAUGCGGCUAGAC-
AUGUCGAAACAUGAUUCACCGAUCAUCAUCAA...
 Codons Identified: Translated into amino acids starting from Methionine (AUG)
and continuing.
 Amino Acid Sequence: M-S-M-R-L-D-M-S-K-H...
 Protein Prediction: Based on start and stop codons, at least one valid protein is
identified.
 Mutation Effect: Mutation introduces an early stop codon, resulting in truncated
proteins.
 Longest Common Substring: GTCATGCCG

You might also like