Index of /ygob/data/v6-Dec2011

      Name                    Last modified       Size  Description


[DIR] Parent Directory        14-Dec-2011 16:05      -  
[TXT] AA.fsa                  06-Dec-2011 18:54  62.4M  
[TXT] Ancestor_genome.tab     06-Dec-2011 18:54   110k  
[TXT] Cglabrata_genome.tab    06-Dec-2011 18:54   767k  
[TXT] Cglabrata_sequence.fsa  06-Dec-2011 18:54  11.9M  
[TXT] Ecymbalariae_genome.tab 06-Dec-2011 18:54   424k  
[TXT] Ecymbalariae_sequenc..> 06-Dec-2011 18:54   9.4M  
[TXT] Egossypii_genome.tab    06-Dec-2011 18:54   595k  
[TXT] Egossypii_sequence.fsa  06-Dec-2011 18:54   8.5M  
[TXT] Klactis_genome.tab      06-Dec-2011 18:54   1.1M  
[TXT] Klactis_sequence.fsa    06-Dec-2011 18:54  10.4M  
[TXT] Lkluyveri_genome.tab    06-Dec-2011 18:54   1.2M  
[TXT] Lkluyveri_sequence.fsa  06-Dec-2011 18:54  11.0M  
[TXT] Lthermotolerans_geno..> 06-Dec-2011 18:54   1.2M  
[TXT] Lthermotolerans_sequ..> 06-Dec-2011 18:54  10.1M  
[TXT] Lwaltii_genome.tab      06-Dec-2011 18:54   1.1M  
[TXT] Lwaltii_sequence.fsa    06-Dec-2011 18:54  10.6M  
[TXT] NT.fsa                  06-Dec-2011 18:54   160M  
[TXT] Ncastellii_genome.tab   06-Dec-2011 18:54   451k  
[TXT] Ncastellii_sequence.fsa 06-Dec-2011 18:54  10.9M  
[TXT] Ndairenensis_genome.tab 06-Dec-2011 18:54   441k  
[TXT] Ndairenensis_sequenc..> 06-Dec-2011 18:54  13.1M  
[TXT] Pillars.tab             06-Dec-2011 19:07   2.4M  
[TXT] README                  24-Apr-2012 15:33     5k  
[TXT] Sbayanus_genome.tab     06-Dec-2011 18:54   544k  
[TXT] Sbayanus_sequence.fsa   06-Dec-2011 18:54  11.6M  
[TXT] Scastellii_genome.tab   06-Dec-2011 18:54   860k  
[TXT] Scastellii_sequence.fsa 06-Dec-2011 18:54  11.0M  
[TXT] Scerevisiae_genome.tab  06-Dec-2011 18:54   1.4M  
[TXT] Scerevisiae_sequence..> 06-Dec-2011 18:54  11.7M  
[TXT] Tdelbrueckii_genome.tab 06-Dec-2011 18:54   405k  
[TXT] Tdelbrueckii_sequenc..> 06-Dec-2011 18:54   8.9M  
[TXT] Tphaffii_genome.tab     06-Dec-2011 18:54   423k  
[TXT] Tphaffii_sequence.fsa   06-Dec-2011 18:54  11.7M  
[TXT] Vpolyspora_genome.tab   06-Dec-2011 18:54   584k  
[TXT] Vpolyspora_sequence.fsa 06-Dec-2011 18:54  14.2M  
[TXT] Xafricana_genome.tab    06-Dec-2011 18:54   439k  
[TXT] Xafricana_sequence.fsa  06-Dec-2011 18:54  10.8M  
[TXT] Xblattae_genome.tab     06-Dec-2011 18:54   458k  
[TXT] Xblattae_sequence.fsa   06-Dec-2011 18:54  13.7M  
[TXT] Xnaganishii_genome.tab  06-Dec-2011 18:54   432k  
[TXT] Xnaganishii_sequence..> 06-Dec-2011 18:54  11.2M  
[   ] YGOB_ALIGNMENTS.tgz     16-Feb-2012 12:58  57.4M  GZIP compressed tar ar>
[TXT] Zrouxii_genome.tab      06-Dec-2011 18:54   1.2M  
[TXT] Zrouxii_sequence.fsa    06-Dec-2011 18:54   9.5M  
[TXT] ncRNA.fsa               06-Dec-2011 18:54    11k  
[TXT] rRNA.fsa                06-Dec-2011 18:54   163k  
[TXT] snRNA.fsa               06-Dec-2011 18:54     3k  
[TXT] snoRNA.fsa              06-Dec-2011 18:54    33k  
[TXT] tRNA.fsa                06-Dec-2011 18:54   773k  


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

    Data from the Yeast Gene Order Browser (YGOB)
 	        Version 6 (Dec2011)

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

 (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:

   V. polyspora Position 1
   T. phaffii Position 1
   X. blattae Position 1 (draft annotation)
   N. dairenensis Position 1
   N. castellii Position 1
   S. castellii Position 1 (old annotation)
   X. naganishii Position 2 (draft annotation)
   X. africana Position 2 (draft annotation)
   C. glabrata Position 1
   S. bayanus Position 1
   S. cerevisiae Position 1
   Ancestral Gene Order
   Z. rouxii
   T. delbrueckii
   K. lactis
   E. gossypii 
   E. cymbalariae
   L. kluyveri
   L. thermotolerans
   L. waltii
   S. cerevisiae Position 2
   S. bayanus Position 2
   C. glabrata Position 2
   X. africana Position 2 (draft annotation)
   X. naganishii Position 2 (draft annotation)
   S. castellii Position 2 (old annotation)
   N. castellii Position 2
   N. dairenensis Position 2
   X. blattae Position 2 (draft annotation)
   T. phaffii Position 2
   V. polyspora 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 [19 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 [18 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
 December 2011 

 Email:	ygob@tcd.ie
 Web:	wolfe.gen.tcd.ie/ygob

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

 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.