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Homework 5

Part 1: Questions regarding Sequence Alignment uses

  1. Since tertiary structure is dependent upon secondary structure, and if we can create a good sequence alignment
    we can compare this alignment to find homologous structures in a database and use those to perhaps predict the
    Tertiary structure. It's almost like an educated guess because you know that if two sequences are very similar
    then their secondary structure must be similar as well, and that extends (albeit not all the time) to the tertiary
  2. If you have one sequence and you purposely add mutations to it, then use sequence alignment to discover how similar
    the two sequences remain (and perhaps extending this to secondary structure examination) you can tell whether or not
    your experiment was a success by seeing how close the alignments are after the fact. I imagine you could even use
    sequence alignment to detect which areas of the sequence are crucial to specific functions within the whole genome
    if for example you introduce mutations, get a really crazy alignment and realize the sequence is no longer viable,
    then you can simply see where the mutations were and declare that area crucial.
  3. If you know the gene sequence that you want to see if it's been transferred, then you could simply do a local-alignment
    and see what you get. If you get a strong alignment, then you can probably say with certainty that the gene has been
    transferred. However you'd have to know where to look, or else you'd be performing tons of local alignments. You also
    could NOT use global alignments because two organisms sequences most likely differ greatly except for the single area of
    contested infection.
  4. Again, by using local alignments on known regulatory sequences and your source sequence, you can see if they're present
    or not by examining whether or not you get a strong alignment from the two. This is useful because a riboswitch for
    example -must- contain an OBS and so if you find out that a specific sequence in your source does in fact code for the
    same OBS, then that riboswitch must be present.
I Attachment History Action Size Date Who Comment
Txttxt r1 manage 2.2 K 2008-11-24 - 07:57 RayAnaya  
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