To Analyse the Dna Sequences of B.Cer Amy Using Computer

Objective  : To analyse the DNA sequences of B.cer Amy using computer

Materials: PC with windows XP

                  :ApE software

Introduction:  After have been trying out the program on my own and still not well familiarizes with the basic features, this time will go on explore on other useful features of this sequence analysis program which is including the locating open frame of the B.cer Amy and translating the DNA sequence into amino acid sequence. In this program also can learn how to align the sequence of the B.cer Amy. Moreover, this program also can analyse the virtual mutation by editing the original sequence of B.cer Amy.

Procedure:

  By launching the ApE program, the open file icon being selected and the sequence file of the B.cer Amy DNA sequences was loaded. This is the DNA sequence for the gene that codes for an enzyme call a-amylase in Bacillus cereus.

Result(Exercise)

1. a) The length of the sequence=1296

b) the start codon =ATG

c)the stop codon=TGA

1. The restriction site for each of these enzyme in the sequence are:

a) EcoRI:0 b) Dral:3 c) BamHI:0  d)  ApoI:4 e)HindIII:0 f) RsaI:4

1. If DNA was digested by by using Psil.

1. The fragment that will produced are 3
2. And the size of these fragment are 909,217,170

Locating ORFs

By selecting the ORFs function from the menu bar, the ORFs map was selected and a new window showed the six possible open reading:

[pic 1]

1. The figure above shown that a reading frame. Reading frame is the possible way to read the nucleotide sequences.
2. The reason why there altogether six reading frames is because 32=6 and three in each direction.
3. In each reading frame, a short vertical line represents the presence of a start codon

while a long vertical line represents a stop codon.

1. The reading frame one is the correct reading frames, Typically only one reading frame is used in translating a gene , and this is often the longest open reading frame. Once the open reading frame is known the DNA sequence can be translated into its corresponding amino acid sequence.  An open reading frame starts with an atg (Met) in most species and ends with a stop codon (taa, tag or tga).
2. By opened the translate at the ORFs icon and all the option being selected will giving below sequence with the amino acid name:

[pic 2]

1. This is the translation of the DNA sequence into its corresponding amino acid sequence. Note that each codon has is made up of three consecutive nucleotides.

a)how many codon: 430

b)how many amino acid:

1. What are the amino acid at these position

1. 10=lysine
2. 85=aspartic acid
3. 218=ile
4. 431=glu

Virtual mutation

1. In the editor window,by  selected nucleotide no 36. Its Changed to an A and translated the new sequence.

[pic 3]

1. The type of mutation is silent mutation and the consequence of the mutation is the codon will change to stop codon.
2. Restore the sequence (Ctrl-Z). Change nucleotide no 13 to an A. will remain constant ile

1. Restore the sequence. Delete the G at position no 61. Will change leu-phe

1. Restore the sequence. Add a C add position no 60. Will change also to leu-phe

Sequence alignment

In this case was learned how align two sequences. This feature is useful when comparing cloasely related genes. By open the new editor window after made some changes both sequences are selected for alignment. A new window opened, displaying the alignment of both sequences to each other.

The Sequence Alignment function compares both sequences and try to match similar stretches of nucleotides. The red areas indicates sequences that could not be matched (mismatches).