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BLAST

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

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BLAST

Postby bandaide » Thu Feb 11, 2010 9:51 pm

Hi everyone!

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:
1.) "Max score". The score of the highest scoring HSP from that
database sequence.

2.) "Tot score". The total score of all HSP's from that database
sequence.


But it still doesn't make sense to me. Can anyone offer a better definition or explain these definitions?

Thanks for your help :)
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Re: BLAST

Postby bandaide » Sat Feb 13, 2010 10:16 pm

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?
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Postby bandaide » Sat Feb 13, 2010 10:42 pm

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.)

Whew. Success.
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Postby Jinky » Mon Aug 22, 2011 6:46 am

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...
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Postby verginov » Wed Sep 21, 2011 11:10 am

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%)
Strand=Plus/Plus

and...

Score = 156 bits (84), Expect = 6e-34
Identities = 84/84 (100%), Gaps = 0/84 (0%)
Strand=Plus/Plus

The Max score is 276 bits and the Total score is 276 + 156 = 432 bits
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