#### README ####

IMPORTANT: Please note you can download correlation data tables, 
supported by Ensembl, via the highly customisable BioMart and 
EnsMart data mining tools. See http://protists.ensembl.org/biomart/martview 
or http://www.ebi.ac.uk/biomart/ for more information.


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Fasta CDS dumps
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These files hold the CDS sequences corresponding to Ensembl Genomes genes

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FILE NAMES
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The files are consistently named following this pattern:
<species>.<assembly>.<eg_version>.<sequence type>.<status>.fa.gz

<species>: The systematic name of the species. 
<assembly>: The assembly build name.
<eg_version>: The version of Ensembl Genomes from which the data was exported.
<sequence type>: cdna for cDNA sequences
<status>
  * 'cds.all' - the super-set of all transcripts resulting from 
     Ensembl known, novel and pseudo gene predictions 


EXAMPLES  (Note: Most species do not sequences for each different <status>)
  for Human:
    Homo_sapiens.NCBI36.cds.all.fa.gz
      cDNA sequences for all transcripts: known, novel and pseudo


Difference between known and novel transcripts
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Transcript or protein models that can be mapped to species-specific entries 
in Swiss-Prot, RefSeq or SPTrEMBL are referred to as known genes in Ensembl.  
Those that cannot be mapped are called novel genes (e.g. genes predicted on 
the basis of evidence from closely related species).


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FASTA Sequence Header Lines
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The FASTA sequence header lines are designed to be consistent across 
all types of Ensembl FASTA sequences.  This gives enough information 
for the sequence to be identified outside the context of the FASTA file. 

General format:

>ID SEQTYPE:STATUS LOCATION GENE

Example of an Ensembl cDNA header:

>ENST00000289823 cdna:known chromosome:NCBI35:8:21922367:21927699:1 gene:ENSG00000158815
 ^               ^    ^     ^                                       ^
 ID              |    |  LOCATION                         GENE: gene stable ID
                 |  STATUS
              SEQTYPE