MF2MAP(1)                  OGMP SEQUENCE UTILITIES                 MF2MAP(1)

NAME
    mf2map - produce gene map coordinates of genes, introns and orfs
             of a given masterfile

SYNOPSIS
    mf2map [-h] [-i size] [-g size] [-t size] [-o ocode] -m masterfile

DESCRIPTION
    The graphical representation of a circular genome map necessitates a file
    that describes the size of each element on the map:

      - genes and exons (clockwise and counter-clockwise)
      - introns (clockwise and counter-clockwise)
      - orfs (clockwise and counter-clockwise)

    Mf2map produces this file from the masterfile given as input. The 
    masterfile is expected to be in a valid format (mf2map runs chkogmp(1) on 
    it to verify this). Mf2map then runs mf2stad(1) to obtain the coordinates
    from which it will compute the size of every item to be displayed on the
    map. Then this coordinate file is checked and invalid annotations are
    removed. Those include:

      - Annotations in incorrect format     
      - Annotations of unknown genes (ie those that don't exist in the file
        /share/supported/apps/ogmp/lib/gene_names.lst (1) )
      - Annotations of mobile elements
      - Annotations of orf's subparts (ex: G-cob-I2-orf246-F2 ==> start )
    
    If mf2map finds two genes that overlap each other (say gene1 and gene2), it
    will remove these two gene annotations and replace them with:

      - An annotation for the part of gene1 not covered by gene2
      - An annotation for the part of gene2 not covered by gene1
      - A special "overlap" annnotation (part covered by both gene1 and gene2)

    Once the cleaning phase is done, mf2map computes the size of every item
    (including the size of the gaps seperating all consecutive items). There 
    are some restrictions on the size that every item must have:

      - Trnas have to be exactly 70bp long
      - Intergenic gaps and the "overlap" slices must be 60 bp long 
      - Every other item must be at least 50 bp long

    Note that these default minimums can all be changed with command line
    arguments (see OPTIONS). When a particular item doesn't meet the size
    requirements, mf2map tries to adjust it. It tries to resize the immediate
    neighbors of the "faulty" item so that it's size can now be increased or
    decreased in order to have a valid size. Mf2map can also decide to resize
    only one of the neighbors of the "faulty" item, but in this case, it must
    have a size of at least 100 nucleotides, otherwise mf2map will not try to
    resize it (this minimum value can be changed via a command line switch).
    If mf2map cannot resize a given slice (generally because the neighboring
    slices are too small), it just leaves it as it is.

    Once the adjustments are done, mf2map produces the file masterfile.prn which
    contains all the information necessary to produce a genome map with charisma.
    Every line in the output file is a comma-separated list of items. The first
    field is always empty (set by user in charisma). The second field is for the 
    markers. The third and fourth are for the sizes of the strands clockwise and
    counterclockwise (if any). The last field is the annotation associated with
    the strand. It will be preceeded by a "+" if the strand is clockwise and by
    a "-" otherwise (gaps are unsigned). All lines end with a "^M" (control-M)
    in order to respect DOS's format restrictions. The first line of the output
    file is the header, which consists of the species associated with the 
    masterfile name and the DNA type (mt, pt, etc...). This header must appear
    in the ouput file if the user plans to run mf2ps on it. It can be removed
    (see OPTIONS) if charisma needs to be run on the output file instead.


OPTIONS
    -i size
       Use size as the minimum size of the gap separating two genes instead
       of the default 70. Note that if two genes overlap, the minimum size
       of the overlaping part is going to be size.

    -g size
       Use size as the minimum size of all genes, exons and introns (default
       50)
       
    -t size
       Use size as the exact size that all trnas must have (default 70).

    -o ocode
       Use ocode as the organism code for the masterfile passed as argument.
       This switch does not have to be used for projects listed in 
       genome_name.lst but is mandatory for those that are not listed in this
       file.
 
    -s size
       Use size as the minimum size that an item must have if mf2map adjusts the
       size of this item (and only this item) in order to allow another one to
       have a valid size (default is 100).

    -h Do not put a header at the top of the output file indicating the species
       and the DNA type (mt, pt, etc...). The header is computed using the
       ocode and appears by default.


FILES 
    /share/supported/apps/ogmp/lib/gene_name.lst
        A description of known mitochondrial genes.
    /share/supported/apps/ogmp/lib/perl/ogmp/gene_names.pl
        A perl library to read and parse the gene_name.lst file.
    /share/supported/apps/ogmp/bin/chkogmp
        A perl program to verify a masterfile's format
    /share/supported/apps/ogmp/bin/mf2stad
        A perl program used to compute the coordinate file
    /share/supported/apps/ogmp/lib/genome_name.lst
        List of all the known projects

SEE ALSO
    ogmp(1), chkogmp(1), mf2stad(1)

AUTHOR
    BF Lang (conception)
    P Rioux (higher-level design)
    N Brossard (detailed design and programming)

Organelle Genome Megasequencing Project.