finding start and stop codon in an insert - (Feb/12/2008 )
Hello molecular biology experts.
This may be stupid question but, i don't know how to find it and this is my first molecular biology experiment.
Here is the story: I have insert in blue script vector and few days ago i prepared the plasmid and got the sequence. Then i used this sequence to find out where the junction is (vector and insert junction) using vector NTI software and then i compared the insert sequence to the sequence that is published (down loaded from NCBI-Gene)-for this purpose i used mRNA, is it right?
Now, my task is to find out the start and stop codon in the insert so, for this do i need to compare the insert with mRNA? and how do i use NTI software to find out these codons.
I hope you guys understand my explanation.
Thanks in advance for your your answers
R.K.B
:mellow
This may be stupid question but, i don't know how to find it and this is my first molecular biology experiment.
Here is the story: I have insert in blue script vector and few days ago i prepared the plasmid and got the sequence. Then i used this sequence to find out where the junction is (vector and insert junction) using vector NTI software and then i compared the insert sequence to the sequence that is published (down loaded from NCBI-Gene)-for this purpose i used mRNA, is it right?
Now, my task is to find out the start and stop codon in the insert so, for this do i need to compare the insert with mRNA? and how do i use NTI software to find out these codons.
I hope you guys understand my explanation.
Thanks in advance for your your answers
R.K.B
:mellow
You don't have to look at the mRNA. Just look for the canonical start codon, ATG, and one of the three stop codons, TAA, TAG, TGA. If your gene is from archaeal bacteria, the start codon might be GTG.
Happy searching!
You can get the NTI program to translate for you. And it will indicate when there is a stop codon. Also you could compare the sequences using the same software.