I am working on an amino acid sequence and because of that reason I use the tool open reading frames (ORFs) of NCBI and I found many results but I need the best result from those so if anyone has any idea suggest to me.
I gues it depends on what type of DNA sequence you have - if you expect that it's coding region and there should be some protein then as Abhijeet Singh said take the longest ORF you find... you can also download different ORFs and try to search them in BLAST and if you will get some nice hit with some homolog sequence then you should have the right ORF.
Hi,
I have a suggestion. First for the subjected gene you should find the conserved domain of the gene in the close similar genotypes. CD can be find in the NCBI. Then use the Expossy or CLC or any othe tools to translate the gene and look for ORF sequences. Now you can have a look on CD and look for the best ORF sequence.
David Morgenstern , best result means the best sequence which would be taken for homology modeling and other insilico perimeters
Nayan Prajapati but how do you know which one is it? assuming you have multiple ORFs per sequence, you might want to try and see what different options give you, especially if you don't have means to look for it in a real sample.
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