This method is used to search for mRNA splice junctions using a weight matrix. The default weight matrix is still that derived from the paper of Mount S.M, (1982) Nucl. Acids Res. 10, 459-472, but we are about to create a whole new set which will be organism specific, and will include them in later releases and make them available via ftp.
The results are displayed in three colours, one colour for each reading frame. The donors are plotted upwards from the base of the panel and the acceptors are plotted downwards from the top of the panel. The donors and acceptors with the same colour are compatible; eg red donors are compatible with red acceptors. Of course it is the combination of reading frame and splice sites that really matters, so donors and acceptors drawn in different colours can be compatible if the reading frame changes. By default all the sites are drawn in the same plot but in the figure shown below they have been separated by reading frame using the programs ability to reorganise the positions of graphical results. This layout of the donors and acceptors is designed to fit with the gene search methods and stop codon plots. The results are plotted as Log-Odds.
The frequency table shown
below is used as a weight matrix and AG and GT are
obligatory at the appropriate positions.
![[picture]](spin_splice.unix.gif.html)
(Click for full size image)
Mount acceptors redone 16-4-91
18 15 0.0 10.0
P -14 -13 -12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3
N 113 113 113 113 113 113 113 113 113 113 113 113 113 113 113 113 113 113
T 58 50 57 59 67 56 58 49 47 66 64 31 34 0 0 11 41 31
C 21 28 34 25 29 33 35 32 42 40 33 25 74 0 0 23 28 41
A 17 11 11 18 7 17 12 23 15 3 10 29 5 113 0 24 21 21
G 17 24 11 11 10 7 8 9 9 4 6 28 0 0 113 55 23 20
Mount donors redone 16-4-91
12 4 0.0 8.0
P -2 -1 0 1 2 3 4 5 6 7 8 9
N 136 136 136 136 136 136 136 136 136 136 136 136
T 28 8 15 17 0 136 9 16 7 84 30 36
C 41 60 16 7 0 0 3 13 3 17 28 39
A 40 56 89 12 0 0 83 91 12 23 53 33
G 27 12 16 100 136 0 41 16 114 12 25 28
This page is maintained by
staden-package.
Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/spin_unix_31.html