CSC

Count Sequence Composition

When a sequence is read into the program its composition is displayed in the Output Window to provide a simple check that the data has been read correctly. The values can also be requested from the "Statistics" menu, when a dialogue will allow subsections of the sequence to be analysed. The results are displayed as shown below.

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Wed 12 Nov 17:10:25 1997: sequence composition
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A 1966 (24.17%) C 1996 (24.54%) G 2185 (26.86%) T 1987 (24.43%) - 0 (0.00%)

Or for protein sequences:
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Mon 14 Oct 17:11:04 2002: sequence composition
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Sequence MYSA_DROME: 1 to 2411
Protein
AA  A     B     C     D     E     F     G     H     I     K     L     M     N    
N  201   0     30    150   281   74    127   45    126   233   243   43    121   
%  8.3   0.0   1.2   6.2   11.7  3.1   5.3   1.9   5.2   9.7   10.1  1.8   5.0   
M  14287 0     3094  17263 36281 10891 7246  6171  14258 29865 27498 5642  13807 

AA  P     Q     R     S     T     V     W     Y     Z     X     *     -    
N  55    167   141   96    93    108   14    63    0     0     0     0     
%  2.3   6.9   5.8   4.0   3.9   4.5   0.6   2.6   0.0   0.0   0.0   0.0   
M  5341  21398 22022 8360  9403  10706 2607  10280 0     0     0     0     
M  5341  21398 22022 8360  9403  10706 2607  10280 0     0     0     0     

Count Dinucleotide Frequencies

This routine simply counts dinucleotide frequencies for the selected region of the sequence. It also calculates an expected distribution based on the base composition. The output looks like:

        A                C                G                T
     Obs    Expected  Obs    Expected  Obs    Expected  Obs    Expected
 A     7.91    5.84     5.64    5.93     5.05    6.49     5.57    5.91
 C     5.91    5.93     5.14    6.02     7.38    6.59     6.10    5.99
 G     6.11    6.49     7.56    6.59     6.30    7.22     6.90    6.56
 T     4.24    5.91     6.18    5.99     8.14    6.56     5.86    5.97