Homework 5

Part 1: Questions regarding Sequence Alignment uses

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
structure.
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.
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.
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	Action	Size	Date	Who	Comment
txt	hw5.pl.txt	manage	2.2 K	2008-11-24 - 07:57	RayAnaya

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