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These are base frequency plots at gene and intron boundaries, in the water flea Daphnia pulex.

Gene components shown are gene start (-20 .. 9 bases around start codon, ATG), gene stop (-9 .. 20 bases around stop codon), intron starts and stops, (+/- 20 bases).

See below data (fasta sequence) and plot files, with perl and R scripts to produce these plots from sequence.

Don Gilbert, July 2007

Daphnia Gene Structure, 1-base frequencies

daphnia-gene-start-1mer daphnia-gene-stop-1mer
daphnia-intron-start-1mer daphnia-intron-stop-1mer



Daphnia Gene Structure, 3-base frequencies

daphnia-gene-start-3mer daphnia-gene-stop-3mer
daphnia-intron-start-3mer daphnia-intron-stop-3mer 
          Genome data sources
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Daphx    : Daphnia pulex NCBI Gnomon predictions (May 2007)
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      Name                          Last modified       Size  Description


[DIR] Parent Directory              23-May-2008 20:39      -  
[TXT] basecount.pl                  04-Jul-2007 17:17     4k  
[TXT] cdsgff2seq.pl                 13-Aug-2007 17:51    22k  
[   ] daphnia-gene-start-1mer.pdf   04-Jul-2007 16:36    15k  
[IMG] daphnia-gene-start-1mer.png   04-Jul-2007 17:22    86k  
[   ] daphnia-gene-start-3mer.pdf   04-Jul-2007 17:02    36k  
[IMG] daphnia-gene-start-3mer.png   04-Jul-2007 17:22    94k  
[   ] daphnia-gene-stop-1mer.pdf    04-Jul-2007 16:39    15k  
[IMG] daphnia-gene-stop-1mer.png    04-Jul-2007 17:22    76k  
[   ] daphnia-gene-stop-3mer.pdf    04-Jul-2007 17:09    55k  
[IMG] daphnia-gene-stop-3mer.png    04-Jul-2007 17:22   123k  
[TXT] daphnia-gene-structure2.html  04-Jul-2007 17:41     2k  
[   ] daphnia-intron-start-1mer.pdf 04-Jul-2007 16:40    14k  
[IMG] daphnia-intron-start-1mer.png 04-Jul-2007 17:22    89k  
[   ] daphnia-intron-start-3mer.pdf 04-Jul-2007 17:10    51k  
[IMG] daphnia-intron-start-3mer.png 04-Jul-2007 17:22   113k  
[   ] daphnia-intron-stop-1mer.pdf  04-Jul-2007 16:42    14k  
[IMG] daphnia-intron-stop-1mer.png  04-Jul-2007 17:22    84k  
[   ] daphnia-intron-stop-3mer.pdf  04-Jul-2007 17:14    51k  
[IMG] daphnia-intron-stop-3mer.png  04-Jul-2007 17:22   120k  
[   ] dpulex1_gnomon_introns.fa.gz  15-Aug-2007 15:59  11.2M  
[TXT] dpulex1gno2-geneend.count     04-Jul-2007 16:08    16k  
[   ] dpulex1gno2-geneend.fa.gz     04-Jul-2007 15:22   797k  
[TXT] dpulex1gno2-genestart.count   04-Jul-2007 16:03    16k  
[   ] dpulex1gno2-genestart.fa.gz   04-Jul-2007 15:30   787k  
[TXT] dpulex1gno2-intronend.count   04-Jul-2007 16:04    21k  
[   ] dpulex1gno2-intronend.fa.gz   04-Jul-2007 15:08   2.3M  
[TXT] dpulex1gno2-intronstart.count 04-Jul-2007 15:59    21k  
[   ] dpulex1gno2-intronstart.fa.gz 04-Jul-2007 15:07   2.3M
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