Input file construction

Simple sample scripts for preparing the input files of DomClust
(.hom and .gene files) using NCBI-BLAST ver.2. Type 'make' to
construct input files using "myco" files in this directory.
After that, type 'make clustering' to invoke DomClust.

To analyze your own sequence data, put all the sequences to be compared
into a file (assuming the file name is <seqfile>), where each sequence
is named as "species_name:gene_name" (see "myco" as an example).

If you have also the result of all-against-all BLAST analysis
for the <seqfile> in the BLAST-tabular format, you can put
the result file as "<seqfile>.blast" on this direcgtory.

Then type
make [clustering] NAME=<seqfile>
to specify your own sequence file.


blast2homfile.pl:	A sample script for converting a BLAST result
			in tabular format (with "-m 8") to a homology
			file for DomClust.

fasta2genefile.pl:	A sample script for converting a sequence file
			in FASTA format to a gene file for DomClust.

myco:	An example of FASTA-formatted sequence file, which contains 
	protein sequences of Mycoplasma genitalium (mge), Mycoplasma
	pneumoniae (mpn), and Ureaplasma urealyticum (uur) genomes.
	Note that the name of each sequence must be of the form
	"species_name:gene_name".
