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Sparseness of b1 data ...
Posted:
Dec 4, 2012 12:38 AM
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You wrote:
?You should probably check them against what you get?
I spot checked against various raw detail files, and I didn?t find any
anomalies.
You wrote:
?It looks like B1 is going to give problems.?
You can probably decide this question by looking at the table at the
end of this post.
To understand this table, you need only realize that to do our subset/
method 2-ways per set per fold per SINGLETON len interval, we need to
have data for a given triple (set, fold, len) in all four categories
determined by subset and method, namely NS, NC, RS, and RC. And the
table shows the counts for the only b1 triples (set, fold, len) for
which all four of NS,NC,RS,RC are non-empty.
So, if you think the counts in the following table are high enough to
allow us to operate on b1, then we?re OK. But if you think they?re
too low, I can very likely increase the counts by getting more
underlying b1 data ... I distinctly recall being conservative when I
picked the b1 proteins and associated messages by assuming that high
amino acid identity meant high codon identity, and this is not
necessarily the case due to the fact that many changes of codons do
not change amino acid identity (e.g. changing att to atc still yields
the amino acid I = ILE = Isoleucine.
Please let me know what you think ? it won?t be a huge detour to try
and pick-up more b1 data if you think the counts in the table below
are too low to allow you to operate satisfactorily.
Finally, what?s very interesting about b1 proteins is that they?re
immunoglobulins, i.e. proteins which play a role in immune systems by
mutating to meet the challenge posed by new antigens (invaders.) So
given the fact that it?s the job of b1 proteins to mutate, it?s
actually surprising we?re getting any counts at all ... in effect, by
their very nature, b1 proteins push the limits of the domain over
which we can expect our hypotheses to hold ...
Table:
Sets F Len NS NC RS RC
1:R1 b1 63 14 14 12 12
1:R1 b1 84 15 14 16 15
2:R2 b1 25 20 19 24 15
2:R2 b1 27 15 15 29 24
2:R2 b1 28 14 12 16 15
2:R2 b1 30 14 15 14 12
2:R2 b1 33 19 12 24 35
2:R2 b1 35 17 16 28 27
2:R2 b1 42 19 18 12 14
2:R2 b1 50 13 14 12 12
2:R2 b1 54 12 13 24 24
2:R2 b1 64 15 16 16 17
2:R2 b1 65 16 16 21 20
2:R2 b1 66 13 14 15 15
2:R2 b1 89 14 14 24 23
2:R2 b1 91 12 12 22 21
2:R2 b1 92 19 18 18 18
2:R2 b1 95 16 16 22 22
2:R2 b1 96 18 18 25 25
2:R2 b1 97 12 12 22 19
2:R2 b1 98 17 17 25 25
2:R2 b1 99 17 17 24 21
2:R2 b1 100 16 15 14 13
2:R2 b1 103 14 14 17 17
2:R2 b1 105 12 12 14 13
2:R2 b1 106 14 13 24 23
2:R2 b1 108 15 14 16 15
2:R2 b1 109 14 12 16 16
3:R3 b1 43 15 15 24 22
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