Question

how to read the percent identity matrix results

Percent Identity Matrix - created by Clusta12.1 1: opossum 2: Guinea 3: Rabbit 4. Racoon 5: Mouse 6: Rat 100.00 77.24 79.31 79.47 79.25 78.73 77.24 100.00 78.92 76.91 77.63 77.56 79.31 78.47 78.92 76.91 100.00 77.89 77.89 100.00 79.96 80.26 78.92 78.90 79.25 77.63 79.96 80.26 100.00 83.75 78.73 77.56 78.92 79.90 83.75 100.00

Answer 1

Percent identity refers to a quantitative measurement of similarity between two sequences ( DNA, amino acid )

Closely related species are expected to have a higher percent identity for a given sequence than distantly related species., and thus percent identity to a degree reflects relatedness.

eg., chimpanzees have highest percent identity with humans

For the above-mentioned sequence, you can read the table as:

	gene1	gene2	gene3	gene4	gene5	gene6
gene1	100.00	77.24	79.31	78.47	79.25	78.73
gene2	77.24	100.00	78.92	76.91	77.63	77.56
gene3	79.31		100.00	77.89	79.96	78.92
gene4	78.47			100.00	80.26	78.90
gene5	79.25				100.00	83.75
gene6	78.73					100.00

the rest of the lower triangular part is just the mirror image (same) of the above shown upper triangular part.

The matrix can be interpreted as :

gene1 and gene1 have 100% similarity (and all the other diagonal elements)

gene1 and gene2 have 77.24% similarity

gene1 and gene3 have 79.31% similarity, and so on.

Therefore the matrix is symmetric M( i, j ) = M( j, i )