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Re: extracting open reading frame (ORF) from a FASTA file

by biosysadmin (Deacon)
on Jul 10, 2005 at 21:23 UTC ( #473795=note: print w/ replies, xml ) Need Help??


in reply to extracting open reading frame (ORF) from a FASTA file

Without giving you the explicit answers, here's some things to think about that you may or may not already know:

  • Don't forget to reverse-complement the DNA sequence and search for reading frames. Look at the reverse and tr functions for some help with that.
  • An ORF is only valid if the start and stop codons are "in-frame," which means that the length of the ORF is divisible by three with no remainder.
  • Most definitions of a valid ORF will not allow any in-frame stop codons. So, for example, the sequence start-start-stop is a valid ORF, but the sequence with start-stop-stop is not. There's exceptions to this (there are always exceptions in biology), but I doubt they are relevant to what you're doing.
Good luck. :)


Comment on Re: extracting open reading frame (ORF) from a FASTA file
Re^2: extracting open reading frame (ORF) from a FASTA file
by Nadiah (Novice) on Jul 11, 2005 at 14:10 UTC
    Hi,
    why is it necessary to reverse complement the dna sequence to search for reading frames? can't we just find the reading frames without doing so?
    and one last question, what are "in- frames"? i'm still not clear about it even after referring to books and other resources.

    thanks!

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