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Forum "ORF finding"

Thread subject: orf

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25 Jun 2016 19:29
Non evaluated contribution

Frame +1 is read on the direct strand of DNA, from 5’ to 3’ while frame -1 is read on the reverse strand, from 3’ to 5’. Size of ORF obtained is 1035bp for frame +1, starting from the 10th nucleotide till 1043 nucleotide, and 129bp for frame -1, starting from 673 nucleotide to 801 nucleotide. However, there are several criteria for an ORF.

ORF must fit the following criteria:
1. do not contain any STOP codons (basic ORF definition...)
2. contains at least 60 codons
3. can be on either direct or reverse strands
4. can be in frames 1, 2 or 3
5. can be incomplete at the 5' or 3' ends, or both!

Following these criteria, only frame +1 fits so it is a valid ORF and will be used for translation and subsequent analysis instead of frame -1.