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