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interpreting sequence alignment

Everything on bioinformatics, the science of information technology as applied to biological research.

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interpreting sequence alignment

Postby helpmeplz » Tue Apr 21, 2009 6:32 pm

http://upload.wikimedia.org/wikipedia/c ... nment2.png

say you have a sequence like that^, how do you interpret it?

i think only the first line is an open reading frame
the second and third line has 'gaps'
4th line is an open reading frame.


is that it? is that all it tells you, whether its an open reading frame or not?

what eslse am i meant to be seeing??

please help..i'm panicing
helpmeplz
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Postby smellor » Wed May 13, 2009 8:16 pm

think about what a sequence alignment is...
in terms of looking for ORF's, you would probably use a tool like Expasy for that, sequence alignments serve a different purpose.
Assuming line 1 and 3 are continuous, as are 2 and 4, what do they tell you?
what does asterisk signify, do you think. what does : signify (think about amino acids E and Q), what does . signify (think about G and S)...
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