gcfiles.ihtml

emboss的linux版本的源代码

The Genetic Code data files are based on the NCBI genetic code tables.
Their names and descriptions are:

<dl>
<dt>EGC.0 </dt><dd>
      Standard (Differs from GC.1 in that it only has initiation site 'AUG')
<dt>EGC.1 </dt><dd>
      Standard
<dt>EGC.2 </dt><dd>
      Vertebrate Mitochodrial
<dt>EGC.3 </dt><dd>
      Yeast Mitochondrial
<dt>EGC.4 </dt><dd>
      Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
<dt>EGC.5 </dt><dd>
      Invertebrate Mitochondrial
<dt>EGC.6 </dt><dd>
      Ciliate Macronuclear and Dasycladacean
<dt>EGC.9 </dt><dd>
      Echinoderm Mitochondrial
<dt>EGC.10 </dt><dd>
      Euplotid Nuclear
<dt>EGC.11 </dt><dd>
      Bacterial
<dt>EGC.12 </dt><dd>
      Alternative Yeast Nuclear
<dt>EGC.13 </dt><dd>
      Ascidian Mitochondrial
<dt>EGC.14 </dt><dd>
      Flatworm Mitochondrial
<dt>EGC.15</dt><dd>
      Blepharisma Macronuclear
<dt>EGC.16</dt><dd>
      Chlorophycean Mitochondrial
<dt>EGC.21</dt><dd>
      Trematode Mitochondrial
<dt>EGC.22</dt><dd>
      Scenedesmus obliquus
<dt>EGC.23</dt><dd>
      Thraustochytrium Mitochondrial
</dl>

<p>

The format of these files is very simple.

<p>   

It consists of several lines of optional comments, each starting with
a '#' character.

<p>

These are followed the line: 'Genetic Code [n]', where 'n' is the
number of the genetic code file.

<p> 

This is followed by the description of the code and then by four lines
giving the IUPAC one-letter code of the translated amino acid, the
start codons (indicdated by an 'M') and the three bases of the codon,
lined up one on top of the other.
   
<p>

For example:

<pre>
   
------------------------------------------------------------------------------
# Genetic Code Table
#
# Obtained from: http://www.ncbi.nlm.nih.gov/collab/FT/genetic_codes.html
# and: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
#
# Differs from Genetic Code [1] only in that the initiation sites have been
# changed to only 'AUG'

Genetic Code [0]
Standard
   
AAs  =   FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
------------------------------------------------------------------------------

</pre>