A Study on DNA Sequence of Rice Using Scoring Matrix Method and ANOVA Technique

Abstract

In this paper, 12 accession numbers of rice has been used. The accession numbers have been taken from the article Cho et al. where it has already been used for other studies. The accession number for DNA, i.e., A, C, G and T along with the gap character (–) have been converted into alignment matrix with 5 rows and 7473 columns. The alignment has been done using ClustalX software. The 7473 columns have been alienated into 5 parts with different dimensions. Later for each part scoring has been done separately. Highest scores from all the 5 parts have been noted down. To minimize the data, the common regions between these 5 parts have been taken into consideration. Later one way ANOVA (Huck and McLean in Psychological Bulletin, 82(4), 511–518,1975; Mukhopadhyay in Applied statistics. Books and Allied (P) Ltd., Kolkata, 2011) has been constructed and conclusions are drawn accordingly.

Appendix

The alignment of matrix (Hertz and Stormo 1999) has been shown with an example. Let us take some DNA sequences of different length say:

• A – A C G T T C C

• A C A C G T A C A

• G C A A G A T – C

• A C A C G T T C C

Gap character (–) come to view when ClustalX software is used. It happens due to multiple sequence alignment.

The above alignment has been created by ClustalX software. Now from the above DNA sequences, the alignment matrix can be formed which has been shown below:

$$ \left[ {\begin{array}{*{20}c} \text{-} & 0 & 1 & 0 & 0 & 0 & 0 & 0 & 1 & 0 \\ A & 3 & 0 & 4 & 1 & 0 & 1 & 1 & 0 & 1 \\ C & 0 & 3 & 0 & 3 & 0 & 0 & 0 & 3 & 3 \\ G & 1 & 0 & 0 & 0 & 4 & 0 & 0 & 0 & 0 \\ T & 0 & 0 & 0 & 0 & 0 & 3 & 3 & 0 & 0 \\ \end{array} } \right] $$

Weight matrix using for the above example is given by:

$$ \left[ {\begin{array}{*{20}c} \text{-} & { - 3.912} & { - 1.040} & { - 3.912} & { - 3.912} & { - 3.912} & { - 3.912} & { - 3.912} & { - 1.040} & { - 3.912} \\ A & {0.759} & { - 1.609} & {1.023} & { - 0.168} & { - 1.609} & { - 0.168} & { - 0.168} & { - 1.609} & { - 0.168} \\ C & { - 1.609} & {0.702} & { - 1.609} & {0.702} & { - 1.609} & { - 1.609} & { - 1.609} & {0.702} & {0.702} \\ G & {0.488} & { - 1.609} & { - 1.609} & { - 1.609} & {1.777} & { - 1.609} & { - 1.609} & { - 1.609} & { - 1.609} \\ T & { - 1.609} & { - 1.609} & { - 1.609} & { - 1.609} & { - 1.609} & {1.374} & {1.374} & { - 1.609} & { - 1.609} \\ \end{array} } \right] $$

The highest weights of the above weight matrix are:

$$ \left[ {\begin{array}{*{20}c} {0.759} & {0.702} & {1.023} & {0.702} & {1.777} & {1.374} & {1.374} & {0.702} & {0.702} \\ \end{array} } \right] $$

Hence the score of the above matrix is:

$$ 0.759 + 0.702 + 1.023 + 0.702 + 1.777 + 1.374 + 1.374 + 0.702 + 0.702 = 9.115 $$

This was a counter example of alignment and weight matrix.