Why does percent similarity only apply to protein alignments? I've been using the EMBOSS NEEDLE to answer questions that I think I did correctly but for some reason I don't understand why the CONCEPT of similarity only applies to protein alignments. (I was comparing two sequence files basically those of you whom may or not know what i'm talking about.) But this is just a broad concept question in my eyes i'm confused... -____- thank you if you can help.
Added by Michael P.
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However, it is more informative and commonly used in protein alignments due to the following reasons: Show more…
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Explain why sequence alignment programs use scoring matrices like the BLOSUM in protein sequence alignment instead of simple yes/no matching. In the BLOSUM matrix, how are "matches" and "mismatches" scored? Explain your answer based on the chemical characteristics of amino acids. How do you determine if a sequence is a good match? What is the importance of the E value and percentage coverage in assessing the quality of match? What protein (super) family does your protein of interest fall into? What evidence do you have from BLAST to support this? Does similarity in sequence prove similarity in function? What are other techniques you can use (computational and lab techniques) to determine if two proteins have similar functions? How can BLAST help you identify the active site of your POI? Make sure to include 2 advantages and 2 disadvantages of the program.
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