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Dna Sequence Translation - Finding Best Orf

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

protein translation orf
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updated by Woa Woa • written by Ana • Ana

4 answers

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

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written by Luwening • Luwening

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

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written by Eric Normandeau Eric Normandeau

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)

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written by Ana • Ana

See the EDIT in my answer for your new interrogation.

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written by Eric Normandeau Eric Normandeau

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!

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written by Ana • 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

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written by Ana • Ana

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.

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written by Lyco Lyco

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.

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written by Woa 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.

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written by Woa Woa

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