ORF-open reading frame?? - (Sep/11/2004 )

ORF is all the possibilities. not all the possibilities will be a gene that results in a protein. each gene has 3 ORFs

smurray, that depends...is it a novel gene, or one that is already known and you just have part? blast can help you line it up if it is one that is in the system. or, based on how much you have, you can translate the possible ORFs and see what they are similar to, or look for conserved sequences to guess what may be the function. to be sure, you'll have to get the whole thing and do studies

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Not quite.

1. Any stretch of DNA sequence has 6 reading frames, three forward, and three reverse.
2. An open reading frame is any segment of that stretch of DNA that begins with a start codon and ends with a stop codon when both the start codon and the stop codon are in the same reading frame.
3. One or many open reading frames can exist on any segment of DNA read in any of the six frames.
4. A gene is an open reading frame that is actually transcribed.
5. The coding region of a gene is that portion of the transcript that is actually translated into a protein.

smurray -- if you translate your dna fragment in all six reading frames, there will be one frame that has no stop codons in it, or has just one at the end of your gene. You can usually find the right frame by inspection, but you can also detect it by BLAST of all the six frames, one of which will be identical to the product of your gene (if it's in the database) or similar to other proteins that are similar to yours.

NCBI's blastx will do this for you. Paste your cDNA sequence into the blastx server (see here) and go!

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thax for the very important informations.

can someone give me some free tools?

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Homebrew, I did not think of the reverse strand

I thought that an ORF just referred to where you started reading the codons; I did not know that you had to have a start and a stop in order to define an ORF? Wow, learn something here every day...thank you for correcting me!

A

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Thanks very much everyone, I'll try it out.

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