Question: Identify restriction sites of a cDNA sequence using a dictionary
0
gravatar for albamaria.muniesa
6.5 years ago by
Spain
albamaria.muniesa0 wrote:

Hi.

I need to identify restriction sites of a cDNA sequence in a fasta file. First, I transform the sequence from FASTA to a string and I have created a dictionary which contains recognition sequences and names of all restriction enzymes.

I want to identify these restriction sites using the dictionary... how can I do that?

Thank you.

ADD COMMENTlink modified 6.5 years ago by Biojl1.7k • written 6.5 years ago by albamaria.muniesa0

Do your restriction sites have different length?

ADD REPLYlink written 6.5 years ago by lelle830

Yes, the sequence contains different restriction sites of different lengths

ADD REPLYlink written 6.5 years ago by albamaria.muniesa0

Than this is really hart to do because you don't know how much of your cDNA string you would want to use as a key for the dictonary (because of the different length). I would vote for trying something similar to waht Torst is suggesting.

ADD REPLYlink written 6.5 years ago by lelle830

Thank you for your answer.

ADD REPLYlink written 6.5 years ago by albamaria.muniesa0
0
gravatar for Torst
6.5 years ago by
Torst960
Australia
Torst960 wrote:

You need to search for each recognition sequence string within the cDNA string.

In python you would use the find() method in the String object: http://www.tutorialspoint.com/python/string_find.htm

 

ADD COMMENTlink written 6.5 years ago by Torst960

How can I do that if my string is a whole cDNA sequence and the dictionary contains ALL retsriction enzymes? I need to identify all the enzymes that cut the sequence...

ADD REPLYlink written 6.5 years ago by albamaria.muniesa0
0
gravatar for Biojl
6.5 years ago by
Biojl1.7k
Barcelona
Biojl1.7k wrote:

Is this a real task for your lab or just some class practice?

If you are in the first case you don't have to reinvent the wheel. This is already implemented in biopython...

http://biopython.org/DIST/docs/cookbook/Restriction.html

 

ADD COMMENTlink written 6.5 years ago by Biojl1.7k

It's a class practice. I've tried to do it with the Restriction module, but I couldn't, so I decided to create a dictionary with the enzymes...

Could you tell me how I should do this practice with the Retsriction module?

ADD REPLYlink written 6.5 years ago by albamaria.muniesa0
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