coding sequences - help, urgent!

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az
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coding sequences - help, urgent!

Post by az » Sat May 20, 2006 1:39 pm

Greetings!

I apologize, if the question seems stupid...

I work with "coding sequences" from NCBI ftp site. The sequences are on FASTA format and their file extension is ffn. I thought that those are supposed to be sequences from the transcibed DNA strand, but if you look at them, the starting codon is ATG and the stop codon is, e.g. TAA. Those codon appear in mRNA codon table... The DNA coding sequence is supposed to contain the complementary triplets, isn't it? I'm really confused :( , because for me it is really important.

Can anybody help me, please ...

daniel.kurz
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Post by daniel.kurz » Sat May 20, 2006 3:14 pm

That is a very weird problem. Is it possible that it was incorrectly saved? Or perhaps it is labled incorrectly?

az
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Post by az » Sat May 20, 2006 3:35 pm

Thanks for reply. But You know, I work with 14 different genomes and I checked some additional ones, it's all the same...

pdavis68
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Post by pdavis68 » Mon May 22, 2006 3:47 am

Well, the RNA start codon is AUG. There is no ATG in RNA because uracil is used instead of thymine.

It depends on how you look at it, though: In DNA you're going to have two strands: ATG on one side and TAC on the other for the start codon. So I guess it depends on which side you're looking at it from.

Pete

az
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Solution

Post by az » Wed May 24, 2006 6:32 am

Thanks for all the replys, I've found the solution, so, may be it will help others:

in NCBI files in ffn format contain mRNA synonimous sequences, i.e. not the transcribed strand ...

Thanks once more

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GreenDog
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Post by GreenDog » Wed May 24, 2006 9:10 am

There is a place where you can choose which strand you want - or +.
"When In Danger Or In Doubt Run In Circles Scream And Shout"
Lawrence J. Peter

az
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Post by az » Sun May 28, 2006 1:06 pm

I'm interested in coding sequences, and they can be either on + or on - strand (as far as I know)

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