Question: Why Default blast search result shows fractional scores at last?
0
gravatar for barathvajramachandran
6.0 years ago by
India
barathvajramachandran0 wrote:

I've runned Blast normally with default parameters. Alignment scores are give in fractions like 84.3. But the BLOSUM 62 matrix contains no fractional scores for any aminoacids..so I would like to know how those fractional score is arrived? http://www.ncbi.nlm.nih.gov/protein/9501247?report=fasta

http://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt

 

blast tool • 1.1k views
ADD COMMENTlink modified 6.0 years ago by Istvan Albert ♦♦ 84k • written 6.0 years ago by barathvajramachandran0
1
gravatar for pld
6.0 years ago by
pld4.8k
United States
pld4.8k wrote:

http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdf

http://www.ncbi.nlm.nih.gov/blast/tutorial/Altschul-1.html

You have to remember that BLAST is not a simple sequence aligner, it tries to find you the likely best hit(s) as quickly as possible. This means BLAST trades accuracy (not precision) for speed, which means it uses many heuristics to speed the search of the sequence space up.

The score isn't an actual alignment score, but a transformation on that score to normalize on the size of the search space and the scoring system used. 

If you just want a raw score, you shouldn't be using BLAST.

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by pld4.8k
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