Figure 1.
Illumina protocol for parallel sequencing of RNA samples as example.
Figure 2.
Communication theoretic model.
In the upper part of the figure the general model is shown, while in the lower part an example is depicted: In particular the messages consist of the numbers which are encoded using the code shown in the green box. In the example the number
is encoded with the code word
. On the receiver side,
is received, which is decoded to the number
. Notice, that this decoding procedure is only rational if we assume that one error is more likely than two errors.
Table 1.
Transition probabilities (76-cycle Ga-II, phiX173, Bustard [15]).
Figure 3.
Influence of distance distribution.
Illustration of codes having the same minimum distance but different distance distributions. The red dot represents the word sent, the black dot the received word , the blue dots are other codewords. In both cases, there is at least one code word with distance
(hence the minimum distance). On the right hand side
can be correctly decoded and assigned to
, while on the left hand side
is assigned to the wrong codeword (the closest blue dot below
).
Table 2.
Addition and multiplication defined on {A,C,G,T}.
Table 3.
Algorithm RndBarcode.
Table 4.
Properties of barcode sets with fixed experimental constraints. The average () and the maximum error (
) are obtained over a non-symmetric channel defined in the Channel Model part.
Figure 4.
Comparison of selected barcodes of length .