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Sequence Analysis Using MUSCLE

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  • #16
    Re: Sequence Analysis Using MUSCLE

    Thanks JJackson.

    How do we know what the start point of the sequence is? Is it where the START codon (AUG) is?

    Is the difference between H1 and H3 numbering dependent on whether the start codon is included in the numbering?

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    • #17
      Re: Sequence Analysis Using MUSCLE

      Originally posted by Sally View Post
      Thanks JJackson.

      How do we know what the start point of the sequence is? Is it where the START codon (AUG) is?

      Is the difference between H1 and H3 numbering dependent on whether the start codon is included in the numbering?
      I don't really know I have always assumed so as it seems the logical place to start. Nearly all my sequence aligning was done years ago on H5N1 where I just got to know the sequences around the areas that were of interest to me (mainly binding and cleavage sites). I have just begun to look at sequences again briefly over the last week or so and H1 is new to me as are the sites and online tools.
      I have just been having a look for a downloadable Bioedit but it seems to no longer be available, however it is so basic it may just run from the executable without needing installing so if any one is interested I can see if it will work like that and upload a copy if it does. It is a lot more basic than most of the current stuff. The CLC (free version) only seems to work with multiple aligned nucleotides when I try to convert to proteins it splits the alignment into individual sequences which you can nolonger see side-by-side.
      Bioedit screen captures before and after Ctrl+G
      Click image for larger version

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      Click image for larger version

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      • #18
        Re: Sequence Analysis Using MUSCLE

        Originally posted by gsgs View Post
        the nucleotide-sequences start with ~50 nucleotides
        which are not decoded to amino-acids.
        Often only parts of these 50 are given or none
        The first occurrance of "ATG" is usually the first decoded amino-acid
        (Methionine,Met,M)

        also niman-H274Y is H275Y in N1
        and D225G is D239G in H1
        Notice what Gs says here about the starting place: the first occurrance of "ATG" = "M"

        So on the MUSCLE alignment example, you will notice their starting positions may vary but consensus starts with the first "atg". See my remarks about counting:

        OK! The example I'm showing has the first "atg" for all three starting at position 9.

        "We see the mutation at position 831 instead of 822;" so if I subtract 8, I'm at position 823... so I'm still 1 off?
        I'm not sure how the counting will work out if we just look at the sequence itself instead of using an alignment program.
        Last edited by mixin; November 30, 2009, 03:55 PM. Reason: spelling
        The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

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        • #19
          Re: Sequence Analysis Using MUSCLE

          in segment 5 it's the 2nd ATG

          what I use:

          Code:
          >A/Index/******/2009/02/01(H1N1)
          XXXXXXXXXXXXXXXXXXXXTAGCAAAAAAGCAGGTCAAATATATTCAAT:ATGGAGAGAATA
          XXAGTTTGTAAAGGGACGTCCAGTAAGCAAAAGCAGGTCAAACCATTTGA:ATGGATGT
          XXXXXXXXXXXXXXXXXXXXXXXTTAGCAAAAAGCAGGTACTGATCCAAA:ATGGAAGACTTT
          XXXXXXAGCAATAACAAGAGCAAAAGCAGGGGAAAACAAAAGCAACAAAA:ATGAAG
          XTTAAGCAAAAGCAGGGTAGATAATCACCTCAATGAGTGACATCGAAGCC:ATGGCGT
          XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAGCAAAAGCAGGAGTTTAAA:ATGAATCCAAACC
          XXXXXXXXXXXXXXXXXXXXCAGGGAGCAAAAGCAGGTAGATATTTAAAG:ATGAGTCTTCT
          XXXXXXXXXXXXXXXXXXXXXXXXAGCAAAAGCAGGGTGACAAAAACATA:ATGGACTCCAA
          start is after the ":"
          there are sometimes differences in the very first or last nucleotides, which I usually
          ignore as supposed sequencing-errors
          I'm interested in expert panflu damage estimates
          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

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          • #20
            Re: Sequence Analysis Using MUSCLE

            Thanks for posting that; it's exactly what we needed.
            Just to clarify,
            I think Gs's example is of all the segments of one virus. We won't be comparing in that same manner; we compare like segments to like: segment 4 with segment 4, etc...

            But this is how the sequences may look when aligned in MUSCLE. Notice how they all align at the ":" but some have fewer letters on the left hand side. MUSCLE begins searching for the mutations at the (":") consensus point.

            Why do we start at the 2nd "atg" in segment 5?
            The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

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