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Re: Re: Re: Re: BioInformatics - polyA tail search

by biosysadmin (Deacon)
on Sep 03, 2003 at 09:27 UTC ( #288554=note: print w/replies, xml ) Need Help??

in reply to Re: Re: Re: BioInformatics - polyA tail search
in thread BioInformatics - polyA tail search

Genome sequence do consist of A's, C's, G's and T's, but sequencing a section of DNA can sometimes give ambiguous results, especially near the end of a sequence. If you can't tell what nucleotide occured at what position in the sequence, it's common practice to use N to denote an ambiguous base.

Lately, sequencing has advanced to the point that while there is still ambiguity in sequencing, the sequencer can narrow down the possible bases. There is a way of denoting this ambiguity with a one-letter code from the IUB ambiguity codes table.

So, like anything in biology there is ambiguity (sometimes). One might even go as far as to say that there is ambiguity about when there is ambiguity, because most sequences that I work on don't contain ambiguous bases. However, the concept of ambiguity can be very useful in a laboratory setting for reasons that are way beyond the scope of this discussion.

Hopefully this cleared up some of the confusion. :)
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Re: Re: Re: Re: Re: BioInformatics - polyA tail search
by Anonymous Monk on Sep 03, 2003 at 12:21 UTC

    Another important use of ambiguity is that sometimes you search sequence ambiguously. So even though the raw DNA only contains {GCAT}, sometimes you are looking for sequences that, at some point, can have restricted sets like {GC} or {AT}.

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