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I need some actual DNA sequences for a computer program.

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I need some actual DNA sequences for a computer program.

Postby Awol » Thu Mar 29, 2012 9:14 pm

I am currently writing a computer program to search DNA sequences. i need some DNA to test my code on. Any ideas where I could get a few thousand pb from?
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Re: I need some actual DNA sequences for a computer program.

Postby wbla3335 » Thu Mar 29, 2012 11:38 pm

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Postby JackBean » Fri Mar 30, 2012 8:19 am

Why do you need actual sequences? Why cannot it be just random?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Postby Awol » Fri Mar 30, 2012 1:10 pm

I have been using random sequences up until now. Its easy enough to pick out a gene looking for start/stop codons (or Shine-Dalgarno sequences) but the 'gene' it identifies is not a multiple of 3 bases.
The program then assumes a deletion/insertion mutation (or equivalent) resulting an erroneous amino acid sequence.
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Postby JackBean » Fri Mar 30, 2012 3:37 pm

Well, he program should read only in-frame start and stop codons.
http://www.biolib.cz/en/main/

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Postby Awol » Fri Mar 30, 2012 3:58 pm

If not sure if I follow what you are trying to say....

If the random sequence is AUGAAAGGUAG (with AUG = Start and UAG = Stop) the 'gene' = AAAGG. Which is
5 bases = 2/3 codons. Where as an actually DNA sequence will tend to have genes of multiples of 3 unless mutated.
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Postby JackBean » Tue May 15, 2012 6:12 am

No, the gene is
AUG AAA GGU AG...
because the STOP codon is not in-frame, it won't be read. It will be like if there was none.
http://www.biolib.cz/en/main/

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Postby JackBean » Tue May 15, 2012 6:12 am

Ane I was trying to point out also, that the START codon AUG is part of the gene ;)
http://www.biolib.cz/en/main/

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