NAME

       fa2dna - format fasta database for use with ANFO

SYNOPSIS

       fa2dna [ option | file ... ]

DESCRIPTION

       fa2dna  reads  one or more files in fasta format and reformats them into a database suitable for anfo(1).
       The input file(s) can contain more than one sequence, and each sequence can be broken  up  into  multiple
       contigs by a stretch of Ns.  All IUPAC ambiguity codes are fully supported.

OPTIONS

       -V, --version
              Print version number and exit.

       -o file, --output file
              Write output to file.file should end in .dna, because anfo and some downstream tools might stumble
              over a different extension.  Default is the genome name with the .dna extension.

       -m N, --maxn N
              Sets  the maximum number of Ns to be interpreted as IUPAC ambiguity codes to N; any longer stretch
              is interpreted as separing contigs.  Default is 2.

       -g name, --genome name
              Sets the genome name to name.  This name is stored in the output file and will be used by anfo  to
              identify  the matched genome in its output.  The genome should be a prefix of the output file name
              to allow downstream tools to find it.  The name should be short, but unique, something like "hg18"
              or "pt2" for human or chimpanzee genomes would work fine.

       -d text, --description text
              Adds text as description to the metadata.  This is purely informational.

       -v, --verbose
              Causes a progress indicator to be printed.

FILES

       /etc/popt
              The system wide configuration file for popt(3).  fa2dna identifies itself as "fa2dna" to popt.

       ~/.popt
              Per user configuration file for popt(3).

BUGS

       None known.

AUTHOR

       Udo Stenzel <udo_stenzel@eva.mpg.de>

SEE ALSO

       anfo(1), fa2dna(1) popt(3), fasta(5)

Applications                                      OCTOBER 2009                                         FA2DNA(1)