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    Data from the Yeast Gene Order Browser (YGOB)
 	        Version 1 (Sep2005)

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 (1) Pillars.tab [1 file]

 This file lists all of the homology pillars used in 
 YGOB with columns for each of the available 
 positions in a pillar.

 These are, from left to right:

   C. glabrata Position 1
   S. castellii Position 1
   S. cerevisiae Position 1
   A. gossypii 
   K. lactis
   K. waltii
   S. kluyveri
   S. cerevisiae Position 2
   S. castellii Position 2
   C. glabrata Position 2

 The order of the columns and the genes is ARBITRARY,
 and does NOT indicate presence on an A or B "track",
 or any syntenic relationships. This file just 
 contains the underlying homology assignments used
 in YGOB. For syntenic information, look at the 
 'Synteny_*.tab' files which are discussed below. Or
 for a locus or region of interest the '+' button in 
 the bottom left hand corner of the YGOB interface 
 will output syntenic information in a tab delimited
 text format. The locus class tables (linked to from
 the trees on the YGOB front page) also assign 
 orthologs and paralogs. 	 
 

 (2) *_genome.tab [7 files]  

 These files are ordered lists of the genes in each 
 of the seven genomes included in YGOB. The columns
 contain, from left to right:

   Gene Name
   Chromosome, Scaffold or Contig Name
   Orientation (W=Watson, C=Crick)  


 (3) Proteins.fsa [1 file] 

 Protein sequences (in FASTA format) for the genes 
 in the above annotation files.


 (4) Synteny_*.tab [4 files]

 These files contain the YGOB syntenic scores for 
 the three post-WGD species at every locus in the 
 given pre-WGD species being used as a scaffold. 

 The columns are, from left to right:

   Synteny Score
   Pre-WGD Outgroup Gene 	
   C. glabrata Track A
   S. castellii Track A
   S. cerevisiae Track A
   S. cerevisiae Track B
   S. castellii Track B
   C. glabrata Track B

 Each position in the six character synteny score 
 represents the syntenic status of the corresponding 
 post-WGD track position, which are, in parallel with 
 the colummns in the file, from left to right:

   C. glabrata Track A
   S. castellii Track A
   S. cerevisiae Track A
   S. cerevisiae Track B
   S. castellii Track B
   C. glabrata Track B

 There are four possible synteny scores:

  1	Syntenic gene presence
  ! 	Non-syntenic gene presence
  0	Syntenic absence
  ?	Non-syntenic absence	

 Genes from two post-WGD species that are both on the
 same Track in this file can be considered orthologs 
 if the synteny score is robust (1 or 0) at all the 
 positions of interest. Similarly genes on Track A 
 in one species and Track B in another are paralogs.  

 Track A and Track B are not equivalent designations 
 across the genome, instead only having a syntenic 
 meaning at the locus being scored, i.e. the A and B
 designations identify orthologs and paralogs at a 
 locus, but the A copy at one locus is not in any way
 connected to the A copy at another locus. 

======================================================

 Kevin Byrne
 September 2005 

 Email:	ygob@tcd.ie
 Web:	ygob.ucd.ie

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 Please read the paper for further details: 

 The Yeast Gene Order Browser: combining curated 
 homology and syntenic context reveals gene fate 
 in polyploid species. 

 Byrne KP, Wolfe KH. 
 Genome Res. 2005 Oct;15(10):1456-61.