====================================================== Data from the Yeast Gene Order Browser (YGOB) Version 5 (Jan2011) ====================================================== (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. Only genes that are turned ON in YGOB are included in this file (OFF genes are not considered to be real features, and hence listing them in pillars on their own would be redundant) 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 genomes included in this version of YGOB. 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 protein coding genes in the above annotation files. (5) NT.fsa [1 file] Nucleotide sequences (in FASTA format) for the protein coding genes in the above annotation files. (6) tRNA.fsa [1 file] Nucleotide sequences (in FASTA format) for the transfer RNA genes in the above annotation files (7) rRNA.fsa [1 file] Nucleotide sequences (in FASTA format) for the ribosomal RNAs in the above annotation files (8) ncRNA [1 file] Nucleotide sequences (in FASTA format) for the non-coding RNA features in the above annotation files (only S. cerevisiae ncRNA features are currently annotated) (9) snRNA [1 file] Nucleotide sequences (in FASTA format) for the small nuclear RNA features in the above annotation files (only S. cerevisiae snRNA features are currently annotated) (10) snoRNA [1 file] Nucleotide sequences (in FASTA format) for the small nucleolar RNA features in the above annotation files (only S. cerevisiae snoRNA features are currently annotated) ====================================================== Dr Kevin Byrne January 2011 Email: ygob@tcd.ie Web: ygob.ucd.ie ====================================================== 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.