This directory has the data for the Feb 2004 freeze of GALA. galGal2 Directory structure: Readme.txt *not available align_3way/ log.chr*.dat.gz alignments/ hg16/ (axtBest) gapchr*.dat.gz localchr*.dat.gz seqfile.dat.gz alternate_genes/ *_Genes.dat.gz *_Genes_exons.dat.gz chromInfo.dat.dat conserved90_hg16.dat.gz conserved80_hg16.dat.gz conserved70_hg16.dat.gz conserved_tfbs/ gg2Hg16/ chr*.gala.gz cpgIsland.dat.gz gcPercent.dat.gz isochore.dat.gz fuguBlat.dat.gz fuguBlat_block.dat.gz cDNA/ *.dat.gz *_block.dat.gz genes/ exons.dat.gz gene_alias.dat.gz gene_cdd.dat.gz gene_dbids.dat.gz gene_expr.dat.gz gene_model_prots.dat.gz *not available gene_ontology.dat.gz *not available gene_orthologs.dat.gz gene_product.dat.gz genename.dat.gz genes.dat.gz godef.dat.gz *not available microRNA.dat.gz *not available multiple_aligns/ predicted_promoters.dat.gz *not available recombRate.dat.gz *not available known_regulatory.dat.gz repeats/ repeatschr*.dat.gz restriction_sites/ chr*.dat.gz *not available rp_multiple/ chr*.3wayRP.dat.gz *not available snp_allele.dat.gz *not available snps.dat.gz tables.txt *not available tissues.dat.gz tfbinding_sites/ chr*.total.gz NOTES on general file format .gz The files were compressed using gzip to save space and download time. .dat The files are comma delimited with text fields enclosed in single quotes. Quotes within text are escaped by doubling them. A Unix newline separates the table rows. NOTES on individual files/tables. alignments - This is a pairwise alignment between galGal2 and the release indicated in the subfolder. There are human alignments. The scoring is done using axtBest. These files can be used to generate lav files. source: http://bio.cse.psu.edu alternate genes - The alternate gene models are represented by pairs of files named after the track name. These are all on freeze galGal2. download source: http://genome.ucsc.edu/ source: tracks by different sources, indicated by name chrom_info - The chromosome name, start, and stop, and species. download source: http://genome.ucsc.edu/ conserved_regions.dat - The regions that are found conserved in the pairwise alignments using strong-hits minus exons from GALA's default set of genes. Three levels are measured 70, 80, 90 percent identity. The alignment is galGal2/hg16 source: http://bio.cse.psu.edu cpgIsland.dat - CpG islands in the galGal2 sequence. source: http://genome.ucsc.edu/ enzyme_info.dat - The enzymes and patterns used for the restriction sites. source: http://www.neb.com/neb/products/res_enzymes/re_update_frame.html gc_percent.dat - The GC Percent track from UCSC for the galGal2 freeze. download source: http://genome.ucsc.edu/ isochore.dat - The GC Percent track from Anton Nekrutenko's Group at PSU genes - The default set of genes are the Refseq genes from the UCSC genenome browser. The Locus Link ID is then used to tie the gene coordinates to more annotations on the genes. Alternately spliced genes have each listed as a separate gene, therefore a we assigned a unique ID to each gene rather than using the Locus Link ID as the primary key. sources: -evid code from LL map data found at ftp.ncbi.nih.gov/genomes/H_sapiens/maps/mapview/elements/LOCUS_objects.gz -genbank files *.gbs ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_N/*.gbs -refseq genes http://genome.ucsc.edu/ -annotations for genes ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz /repository/UniGene/Hs.data.gz /repository/OMIM/genemap http://expression.gnf.org/cgi-bin/index.cgi repeats - Repetitive elements. download source: http://genome.ucsc.edu/ restriction_sites - Matches to the enzyme pattern for 128 enzymes on the hg16 sequence. source: http://bio.cse.psu.edu snpall.dat - snps.dat - sources: http://genome.ucsc.edu/ files:bgisnp.txt.gz tables.txt - The table definitions. The field types are listed as integer which is from -2,147,483,648 to 2,147,483,647. varchar(N) which is a character field with up to N characters. smallint with is from -32,768 to 32,767. Fields generated from other fields have the equation used to generate the values and are used for indexing. tfbinding_sites - Matches to 166 transcription factor matrices. The matrices come from Transfac (registration required). These are matches on the galGal2 sequence of 75% or better. source: http://bio.cse.psu.edu