enhancerfinder Files

This directory contains compressed directories of genomes of several organisms. 
The data for each genome was derived from the NCBI .gbk files that describe the
chromosomes of that species. The .txt files are our compression of these files. 

The master.txt file gives the names of the chromosomes of the organism, as well
as the name of the organism (sometimes a nickname).

The genome.txt file gives the sequence of nucleotides in the organism's genome, 
encoded 2 bits per nucleotide.
 
The exceptions.txt file lists all the locations where an N was specified in the
NCBI version of the genome. Since only two bits are used per nucleotide, these
N's appear to be the nucleotide A. But use of the exception file enables the
enhancer program to ignore any matches that utilize N's the the NCBI version
of the genome.

The file xcontigs.txt tells where each contig (.gbk file) is mapped into the
final genome, and which chromosome is represented. In some genomes, a 
chromosome is represented by several contigs, but in the case of the species
given here, each chromosome is represented by one contig. 

The xmrnadata.txt file contains the nucleotides for each gene in the organism.
Each alternative splice of every gene is represented.

The xmrnastart.txt file contains, for every alternative splice, the gene number
and where that splice starts in the xmrnadata.txt file.

The xallnames.txt file gives all the names of the genes in the organism. Each 
entry contains a name and the gene number. Most genes have several recognized 
names.

The utrinfo.txt file is not used in the current enhancer program. It is 
there for possible future use.

The file enhancer.exe is an executable file of the enhancer program 
constructed to run on a MAC.  It is exactly the file which would be
built from the code in the programs directory. However, you should execute the 
command "chmod a+x enhancer.exe" to make sure that enhancer is executable (in
some systems, the execution permission is deleted by the unzip procedure for
security purposes).

To construct the enhancer program for other platforms, download the 
programs.zip file, unzip it, and build the enhancer program using the
command "makefile -f make.enhancer".

After running enhancer, the details of the clusters found in the most recent 
run is found in the file hashresults. Before running enhancer again, if you
want to preserve the details of your most recent enhancer run, move 
hashresults into a different file.