Table 2.
Alignment scores for PFE0920c protein of P. falciparum and yeast cyclin, P40186, with PfSSM series
| Clustering (%) | Smat | SSmat | PfFmat | PfFSmat |
|---|---|---|---|---|
| 50 | 116.4 (124) | 74.4 (128) | 106.3 (124) | 37.0a, 35.6 |
| 60 | 116.0 (124) | 75.2 (128) | 107.7 (124) | 36.7a, 35.3 |
| 70 | 116.2 (124) | 75.3 (128) | 108.2b (124) | 37.7a, 36.1 |
| 80 | 117.8b,c (124) | 79.6 (128) | 103.2 (122) | 37.9 (190) |
| 90 | 114.2 (124) | 90.1b (128) | 98.9 (124) | 39.4b (190) |
aThe scores of the first hit from a different organism.
bThe highest obtained scores for the respective columns.
cThe score for the best performing matrix series.
The first column of the table represents the clustering percentage at which the matrices (represented in the subsequent columns along the first row) were calculated. Columns 2–5 represent the alignment scores obtained for each matrix series at different clustering percentages. The value in the closed bracket is the amino acid overlap for the alignment. The values represented with ‘a’ are the cyclin family first hits obtained from a different organism and the values following it are the yeast cyclin hits which take up a second position. We did not mention the overlap lengths for these instances. The standard equivalent matrix values for each corresponding ‘b’ marked cells from column 2–5 are 112.4 (128), 96.1 (124), 101.9 (124) and 54.7(55), respectively. Smat = Symmetric matrix; SSmat = Symmetric Scaled matrix; PfFmat = Plasmodium falciparum Fixed matrix; PfFSmat =Plasmodium falciparum Fixed Scaled matrix.