This directory contains the files for GALA, mouse Oct 2003 release.

Directory structure:
	Readme.txt -- This file
*not available        align_3way/
                log.chr*.dat.gz
        alignments/
                gapchr*.dat.gz
                localchr*.dat.gz
		seqfile.dat.gz
        alternate_genes/
                *_Genes.dat.gz
                *_Genes_exons.dat.gz
        binding_sites/
                total*.dat.gz
        chrom_info.dat.gz
        conserved70.dat.gz
        conserved80.dat.gz
        conserved90.dat.gz
*not available        conserved_tfbs/
                chr*.dat.gz
	cpgIsland.dat.gz          
        enzyme_info.dat.gz
        gcPercent.dat.gz
        genes/
                gene_dbids.dat.gz
                mprot.dat.gz
                exons.dat.gz
                gene_ontology.dat.gz
                prod.dat.gz
                expression.dat.gz
                genename.dat.gz
                tissue_info.dat.gz
                gene_alias.dat.gz
                genes.dat.gz
                gene_expr.dat.gz
                gene_cdd.dat.gz
                go_defs_info.dat.gz
                gene_orthologs.dat.gz
*not available        lscores/
                chr*_Lscore.dat.gz
*not available        multiple_aligns.dat
*not available        mult_align_segments.dat
*not available        promoter_func.dat.gz
*not available        recombRate.dat.gz
	repeats/
		repeatschr*.dat.gz
	restriction_sites/
		chr*.dat.gz
*not available	rp/
		chr*.regpotent.dat.gz
*not available	rp_multiple/
		chr*3wayRP.dat.gz
        snpall.dat.gz
        snps.dat.gz
	tables.txt

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 mm4 and hg16.  The scoring is 
	done using axtNet.  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 mm4.
	download source: http://genome.ucsc.edu/
        source: tracks by different sources, indicated by name
binding sites -
	Matches to 164 transcription factor matrices.  The matrices come
	from Transfac (registration required).  These are matches on the 
	mm4 sequence of 75% or better.
	source: http://bio.cse.psu.edu
chrom_info -
	The chromosome name, start, and stop, and species.
     	download source: http://genome.ucsc.edu/
conserved*.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.
        source: http://bio.cse.psu.edu
cpgIsland.dat -
	CpG islands in the mm4 sequence.
	source: http://genome.ucsc.edu/
enzyme_info -
	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 mm4 freeze.
        download source: http://genome.ucsc.edu/
genes - 
	The default set of genes are the Locus Link genes from the genbank
	summary files.  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.  Any genes in the RefSeq track at UCSC that are not in 
	the set from the genbank files are added.
	sources:
	-evid code from LL map data found at
	ftp.ncbi.nih.gov/genomes/M_musculus/maps/mapview/elements/LOCUS_objects.gz
	-genbank files *.gbs
	ftp.ncbi.nih.gov/genomes/M_musculus/CHR_N/*.gbs
	-refseq genes
	http://genome.ucsc.edu/
	-annotations for genes
	ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz
			/repository/UniGene/Mm.data.gz
			/repository/OMIM/genemap
	http://expression.gnf.org/cgi-bin/index.cgi
        http://www.jax.org/
lscores -
	Log likelyhood scores on conservation.
	source: http://genome.ucsc.edu/
recombRate.dat -
	Recombination rates as calculated by deCODE Genetics, Genethon,
	and Marshfield.
	download source: http://genome.ucsc.edu/
repeats -
	Repetitive elements.
	download source: http://genome.ucsc.edu/
restriction_sites -
	Matches to the enzyme pattern for 128 enzymes on the mm4 sequence.
	source: http://bio.cse.psu.edu
snpall.dat -
snps.dat -
	The Single Nucleotide Polymorphisms.  
	sources: ftp.ncbi.nih.gov/snp/mssql/data/SubPopAllele.gz, 
                                   "            /ANSI1_flat/ds_flat_chN.flat.gz
	 	 http://genome.ucsc.edu/  files:snpNih.txt.gz, snpTsc.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.