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    Data from the Yeast Gene Order Browser (YGOB)
 	        Version 3 (Apr2009)

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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:

   K. polysporus Position 1
   S. castellii Position 1
   C. glabrata Position 1
   S. bayanus Position 1
   S. cerevisiae Position 1
   Ancestral Gene Order
   Z. rouxii
   K. lactis
   A. gossypii 
   S. kluyveri
   K. thermotolerans
   K. waltii
   S. cerevisiae Position 2
   S. bayanus Position 2
   C. glabrata Position 2
   S. castellii Position 2
   K. polysporus 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 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. 
 

 (2) *_genome.tab [12 files]  

 These files are ordered lists of the genes in each 
 of the twelve genomes included in YGOB Version 3. 
 The columns contain, from left to right:

 - NAME - unambiguous name used to identify the gene
 - ORIENTATION - 0 = Crick Strand, 1 = Watson Strand
 - START COORDINATE - 5' start of the co-ordinate range of the feature
 - STOP COORDINATE - 3' end of the co-ordinate range of the feature
 - ON/OFF - whether feature is displayed or not in YGOB
 - CHROMOSOME/CONTIG/SCAFFOLD NUMBER - identifying number of source sequence
 - SHORT NAME - the shorter name that will appear in the gene box on screen in YGOB
 - COORDINATES - complete gene co-ordinates with intron/exon annotation and complement tag if appropriate
 - NOTES - GenBank tags, SGD descriptions and notes for the locus

 The only exception being the 'Ancestor_genome.tab' file as
 the ancestral gene order has no underlying sequence and hence
 no co-ordinates. In this case the columns are:

 - NAME - unambiguous name used to identify the gene
 - ORIENTATION - 0 = Crick Strand, 1 = Watson Strand (inferred from homologs)
 - ON/OFF - whether feature is displayed or not in YGOB
 - CHROMOSOME NUMBER - identifying number of ancestral chromosome
 - SHORT NAME - the shorter name that will appear in the gene box on screen in YGOB


 (3) *_sequence.fsa [11 files]  

 The nucleotide sequences (in FASTA format) of the 
 chromosomes, contigs or scaffolds (denoted by 'Chr', 
 'c' and 's' prefixes, respectively - which one is used 
 depends on the particular genome assembly) from each of
 the genomes featured in YGOB Version 3 (the ancestral 
 gene order has no underlying sequence).


 (4) AA.fsa [1 file] 

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


 (5) NT.fsa [1 file] 

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


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

 Dr Kevin Byrne
 April 2009 

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

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 Please read the papers for further details: 

 Additions, losses and rearrangements on the 
 evolutionary route from a reconstructed ancestor 
 to the modern Saccharomyces cerevisiae genome

 Gordon JL, Byrne KP, Wolfe KH.
 PLoS Genet. 2009 May;5(5):e1000485.


 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.