README file for ftp_genome and genome_primer.


OVERVIEW:

genome_primer provides a web interface for genome-annotation-directed
PCR primer design using the AnyPrimer APIs for primer3 and e-PCR.  It is included
with this distribution as an example application of the AnyPrimer libraries

ftp_genome is used to retrieve GenBank files, parse annotations
and format files to be used for by genome_primer.

NOTE: These demonstration scripts are written for *nix webservers.  
Some of the code would have to be edited for other OSs (in particular,
expressions with the backtick [`] operator). 


LIBRARIES USED:

CGI
Net::FTP
Bio::SeqIO
AnyPrimer


INSTALLATION AND USAGE:

Once installed, hard-coded user info must be edited in the scripts

ftp_genomes:

- location of species root directory, where new directories for each species
  will be created
- email for anonymous ftp password

genome_primer:

- location of AnyPrimer libraries (if not in default location)
- location of species root directory


genome_primer is perl/CGI web application that is ready to use 
as-is with the example species.  If different genomes 
are required, they may be obtained using ftp_genome.  You will also
have to edit the select menu to add your species name

Install the genome_primer script in your CGI or modperl directory
(default location in RedHat linux is /var/www/cgi-bin)

ftp_genome can be used to download genomes from NCBI.  All genomes in
a specified directory may be downloaded [-f option], or a single genome
[-s species_name].  The -n option specifies downloading of genomes that
have not been previously downloaded and processed.

ftp_genome downloads GenBank accessions and parses out the sequence and features
to create the following files required by genome_primer:

*.genes    - list of genes and genomic coordinates
*.fa       - fasta format DNA file of complete genome
*.gff.gz   - zipped flat file with GFF annotations



