February 11, 2010 at 9:51 pm #12749
I’m a little confused about some categories in NCBI’s Blast. I did a nucleotide Blast. In the "Description" section it gives me a Max score and a Total score. I know how the BLAST score is calculated, but I don’t understand how these two values are derived.
I’ve been doing some googling and I find definitions like this:quote :
But it still doesn’t make sense to me. Can anyone offer a better definition or explain these definitions?
Thanks for your help 🙂
February 13, 2010 at 10:16 pm #97584
I found this page that gives the definitions of total score and max score: http://www.digitalworldbiology.com/BLAST/slide7.html
I just wish I had some one explain to me how the total score can be bigger than the max score. I need an example you know?
February 13, 2010 at 10:42 pm #97585
Okay I figured it out! If two sequences are not side by side, the max score is the score of the longest matching sequence. (For instance, if you are searching for primer matches, the longest primer that matches will determine the max score.) The total score is the sum of all of the sequences that match. (So again, it would add the scores of the primer that matched near the 5′ end and the primer that matched near the 3′ end.)
August 22, 2011 at 6:46 am #105997JinkyParticipant
As I know, BLAST is one of the most widely used bioinformatics programs, because it addresses a fundamental problem and the algorithm emphasizes speed over sensitivity. This emphasis on speed is vital to making the algorithm practical on the huge genome databases currently available, although subsequent algorithms can be even faster.See more wikipedia.com…
September 21, 2011 at 11:10 am #106398verginovParticipant
Let’s say it with another words. If the BLAST hit has more than one high-scoring segment pair (HSP), the Total score will have greater value than the Max score and will be equal to the sum of the bit-scores of all HSPs. A short example from my sequence searches via BLASTn:
I have a subject sequence containing two HSPs with the following statistics
Score = 276 bits (149), Expect = 4e-70
Identities = 149/149 (100%), Gaps = 0/149 (0%)
Score = 156 bits (84), Expect = 6e-34
Identities = 84/84 (100%), Gaps = 0/84 (0%)
The Max score is 276 bits and the Total score is 276 + 156 = 432 bits
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