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Splice site search

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.

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.

[picture]
(Click for full size image)

The frequency table shown below is used as a weight matrix and AG and GT are obligatory at the appropriate positions.

  Mount donors redone 16-4-91
      12     3   -16.085    -7.500
  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
  Mount acceptors redone 16-4-91
      18    15   -26.142   -14.400
  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

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/nip4_27.html