Dna Sequence Translation - Finding Best Orf

Question

[Ana]

Hello!

I'm a biology student and I have a question:

I have given a DNA sequence and I have to find the amino-acids sequence. How do I decide which is the right ORF (Open Reading Frame) for the translation? Can you suggest a program that will help me do that? It could be on NCBI page!

Thank you!

AA

Answer 1

[Luwening]

you may try a gene predict program, http://en.wikipedia.org/wiki/Gene_prediction

Answer 2

[Eric Normandeau]

Hi,

You can use ORF Finder on the NCBI website.

Otherwise, a Google search with "ORF Finder" will list you other possibilities.

EDIT: Once you have passed your sequence through the ORF Finder, it is up to you to decide which ORF is the more probable. Your choice should be based on the presence of START and STOP codons, as well as on the total length of the ORFs found.

Cheers

[Ana]

thank you!

so i have to use all possible reading frames to translate the sequence? there is no way to find which is the right one? (Sorry if my question is stupid.. I'm new at this and a bit confused)

[Eric Normandeau]

See the EDIT in my answer for your new interrogation.

[Ana]

i chose the longest one and then -as suggested above- i had a blastp so i got my results. I also tried blastx and tblastx and i had the same results so i guess that all the 3 ways work the same for my query and they are all correct to use! is that true?

Thanks again!

[Ana]

*let me explain that i know which organism my sequence is from so that's why i'm saying that i have a specific result that i consider it correct

Answer 3

[Lyco]

Try to use the program ESTscan whch uses coding propensities similar to those used by the GenScan program. There is also a web server that offers propensity data for mammals and fungi, it might be possible to find others on the web. Ths program is excellent for deciding on which reading frame is most likely to be real, it can also compensate for occasional frameshift errors.

Answer 4

[Woa]

Of the all possible ORFs a 'good' one will be possibly longer, and if it doesn't code for a novel protein, will have a decent blastp hit as judged by evalue/score.

[Woa]

FOr finding out the ORFs use the EMBOSS package and tools that come with it like 'GETORF' and 'SIXPACK'. Note that there are two definitions of ORF: stop-to-stop and start-to-stop.