I need some actual DNA sequences for a computer program.

[Awol]

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?

[wbla3335]

http://www.ncbi.nlm.nih.gov/genbank/

[JackBean]

Why do you need actual sequences? Why cannot it be just random?

[Awol]

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.

[JackBean]

Well, he program should read only in-frame start and stop codons.

[Awol]

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.

[JackBean]

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.

[JackBean]

Ane I was trying to point out also, that the START codon AUG is part of the gene