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What is the difference between different variants of BLOSUM matrices?

e.g What is the difference between BLOSUM 30 and BLOSUM 62?

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    $\begingroup$ Welcome to SE Biology. Please finish reading the Tour. You will often find that your questions have already been answered. For example, does this answer help you? If not, try to find the answer yourself first. Wikipedia is often the first place to look. If you still have difficulties with the explanations, then post them explaining your problem. $\endgroup$
    – David
    Apr 28 '20 at 20:02
  • $\begingroup$ Thanks @David. I didn't see that. And could you please tell me are there specific instances I would use BLOSUM30 or BLOSUM62 ? Why should not I always choose BLOSUM90? $\endgroup$
    – HBashanaE
    Apr 29 '20 at 8:01
  • $\begingroup$ Thanks @mgkrebbs. I didn't see that. And could you please tell me are there specific instances I would use BLOSUM30 or BLOSUM62 ? Why should not I always choose BLOSUM90? $\endgroup$
    – HBashanaE
    Apr 29 '20 at 8:02
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    – David
    Apr 29 '20 at 21:30
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BLOSUM is a substitution matrix employee for protein sequence alignments, which are based on maximum identity percentage of the aligned protein sequences used in calculating them. For example, BLOSUM30 would correspond to alignments with a maximum of 30% of identity, BLOSUM62, for a 62% of identity. The type of matrix depends on the study your are doing. BLOSUM62 is the most widely used matrix for phylogenetic analysis. BLOSUM90 would return sequences with 90% of identity. The percentage of identity is related to the phylogenetic distance, and this to the variations in the protein sequences,therefore BLOSUM90 cannot always be used. That is why you must take into account the type of analysis you are going to perform. (https://en.m.wikipedia.org/wiki/BLOSUM)

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  • $\begingroup$ Thanks @Armand Could you please tell me are there specific instances I would use BLOSUM30 or BLOSUM62? Why should not I always choose BLOSUM90? $\endgroup$
    – HBashanaE
    Apr 29 '20 at 7:57

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