Hi everyone! It's my first approach to BLAST and to comparative genomics, and I would appreciate some help. I understood the theoric part of what these values rapresents (max score/%identities etc), but then, doing the pratical part, I have some problems. How can I actually understand if these values are ok or not? To be more clear, I will report some values so that you will understand better.
The query lenght is 370 aa The max score and total score is 340 The query cover is 97% The e-value is 1e-103 And the percentage identity is 47.45%
Now, I understand that is a good allignment, but I would appreciate so much if someone could explain me in a simple way for example HOW I can understand that the score I got is an High one, or just simply how you would interpret these datas. And more, how is the percent. identity related to matrice (BLOSUM 62) I used? WHY is this a good value?
I know I probably made some silly questions, but as I said, it's my first approach and I'm trying to understand the basis. Thank you so much to everyone that will help.
NCBI has several resources available on this page that should be useful. Statistics of sequence similarity scores is covered here.
Genomax's linked resources are all you should need to know, but the TL;DR is that these statistics tell you different things about how accurate/meaningful your alignment is. Coverage for example, tells you whether you have a short or long alignment, and combined with identity can tell you whether you have a long, low identity match (e.g. perhaps an orthologous genes), or a short, high identity match (similar protein domains/active sites). The E-value is a description of how likely it is that the match could have arisen effectively by chance, so you want this number to be as low as possible. A lot of people/tools use a default of 1E-6, but this is pretty arbitrary.
Thank you so much to both of you.. Joe could you apply what you said to my example? In my specific case how are these two parameters related? Again, sorry if it's a banal question, but this is all new and math is not my strong point and material example help me in understanding. Thank you so much for your time!!!