More information is available at http://faculty.cs.tamu.edu/shsze/gcquery.

INSTALLATION

1. Type ./install to install gcquery.

2. Either move the executable files gcquery, formatdb, blastall to a directory
   on the search path or add the current directory to the search path.

3. Type ./runquery to test the software.

INPUT

The following files are needed:

1. A file that specifies the query gene cluster. This file contains gene names
   and protein sequences in FASTA format. 

   Example: query.faa

2. One or more FASTA files that contain all gene names and protein sequences
   on each chromosome of the target genome.  Genes within each FASTA file
   should be in the same order as on the chromosome (.faa files on the NCBI
   website can be used directly). 

   Example: NC_008536.faa 

USAGE

   gcquery -q query.faa -d chr1.faa chr2.faa -c 1 -b 1e-7 -e 1e-5 -o result.txt 

Command line parameters:

   -q "file name containing query cluster"
   -d "file names containing all gene names and protein sequences on each chromosome"
   -c "type of genome (0 - linear; 1 - circular)"
   -b "BLAST e-value cutoff"
   -e "GCQuery e-value cutoff"
   -o "output file name"

OUTPUT

Clusters found are displayed with e-value from low to high.  For each cluster,
"Expect" gives the e-value, "size" gives the number of genes in the cluster,
and "chromosome" gives the file name of the target chromosome.  Each of the
following rows shows one gene that is in the cluster.  After the gene name,
its location on the chromosome is given, and each of its related genes from the
query and the corresponding protein-protein BLAST e-value are shown in
parentheses.  


Example: result.txt

Gene clusters found in Solibacter usitatus Ellin6076 from the query operon
mraZW-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ of E. coli K12.