METHODS

OPTIONS

  Option      Description                      Default
  ------      -----------                      -------

  -fgcolor      Foreground color               black

  -outlinecolor Synonym for -fgcolor

  -bgcolor      Background color               turquoise

  -fillcolor    Synonym for -bgcolor

  -linewidth    Line width                     1

  -height       Height of glyph                10

  -font         Glyph font                     gdSmallFont

  -connector    Connector type                 0 (false)

  -connector_color
                Connector color                black

  -label        Whether to draw a label        0 (false)

  -description  Whether to draw a description  0 (false)

  -strand_arrow Whether to indicate            0 (false)
                 strandedness

  -hilite       Highlight color                undef (no color)

In addition, the following glyph-specific options are recognized:

  -draw_dna     If true, draw the dna residues        0 (false)
                 when magnification level
                 allows.

  -draw_target  If true, draw the dna residues        0 (false)
                 of the TARGET sequence when
                 magnification level allows.
                 See "Displaying Alignments".

  -draw_protein_target  If true, draw the protein residues        0 (false)
                 of the TARGET sequence when
                 magnification level allows.
                 See "Displaying Alignments".

  -ragged_extra When combined with -draw_target,      0 (false)
                draw extra bases beyond the end
                of the alignment. The value is
                the maximum number of extra
                bases.
                See "Displaying Alignments".

  -ragged_start  Deprecated option.  Use
                 -ragged_extra instead

  -show_mismatch When combined with -draw_target,     0 (false)
                 highlights mismatched bases in
                 the mismatch color.  
                 Can be 0 (don't display);
                 1 (display when the DNA fits);
                 or another positive integer
                 (display when the region in
                 view is <= this value).
                 See "Displaying Alignments".

  -mismatch_only When combined with -draw_target,     0 (false)
                 draws only the mismatched bases
                 in the alignment. Implies
                 -show_mismatch.
                 See "Displaying Alignments".

  -mismatch_color The mismatch color to use           'lightgrey'

  -insertion_color The color to use for insertions    'green'
                   relative to the reference.          

  -deletion_color The color to use for deletions      'red'
                  relative to the reference.

  -indel_color   The color to use for indels, used   'lightgrey'
                 only if -insertion_color or
                 -deletion_color are absent

  -true_target   Show the target DNA in its native    0 (false)
                 (plus strand) orientation, even if
                 the alignment is to the minus strand.
                 See "Displaying Alignments".

  -realign       Attempt to realign sequences at      0 (false)
                 high mag to account for indels.
                 See "Displaying Alignments".

If the -draw_dna flag is set to a true value, then when the magnification is high enough, the underlying DNA sequence will be shown. This option is mutually exclusive with -draw_target. See Bio::Graphics::Glyph::generic for more details.

The -draw_target, -ragged_extra, and -show_mismatch options only work with seqfeatures that implement the hit() method (Bio::SeqFeature::SimilarityPair). -draw_target will cause the DNA of the hit sequence to be displayed when the magnification is high enough to allow individual bases to be drawn. The -ragged_extra option will cause the alignment to be extended at the extreme ends by the indicated number of bases, and is useful for looking for polyAs and cloning sites at the ends of ESTs and cDNAs. -show_mismatch will cause mismatched bases to be highlighted in with the color indicated by -mismatch_color. A -show_mismatch value of "1" will highlight mismatches only when the base pairs are displayed. A positive integer will cause mismatches to be shown whenever the region in view is less than or equal to the requested value.

At high magnifications, minus strand matches will automatically be shown as their reverse complement (so that the match has the same sequence as the plus strand of the source dna). If you prefer to see the actual sequence of the target as it appears on the minus strand, then set -true_target to true.

Note that -true_target has the opposite meaning from -canonical_strand, which is used in conjunction with -draw_dna to draw minus strand features as if they appear on the plus strand.

Displaying Alignments

Without additional help, this glyph cannot display gapped alignments correctly. To display gapped alignments, you can use the Bio::Graphics::Brower::Realign module, which is part of the Generic Genome Browser package (http://www.gmod.org). If you wish to install the Realign module and not the rest of the package, here is the recipe:

  cd Generic-Genome-Browser-1.XX
  perl Makefile.PL DO_XS=1
  make
  make install_site

If possible, build the gbrowse package with the DO_XS=1 option. This compiles a C-based DP algorithm that both gbrowse and gbrowse_details will use if they can. If DO_XS is not set, then the scripts will use a Perl-based version of the algorithm that is 10-100 times slower.

The display of alignments can be tweaked using the -ragged_extra, -show_mismatch, -true_target, and -realign options. See the options section for further details.

There is also a -draw_protein_target option, which is designed for protein to nucleotide alignments. It draws the target sequence every third base pair and is supposed to align correctly with the forward and reverse translation glyphs. This option is experimental at the moment, and may not work correctly, to use with care.