Please send any comments, suggestions, and bug reports to symap@agcol.arizona.edu.

Version 2.0

Release date: 5/18/07
This release includes many new features for the alignment view. The dot plot view was not changed.

New Features Block view (CGI):

• View reverse option: reverse which of the two genomes is the reference genome.
• Chromosome view: the blocks are color coded to indicate which chromosome they are from. Also, the number of anchors is displayed over each block.

New Features on Java interface:

• Filters:
  • For a given track (Block, Hit, Sequence) hover the mouse over the track and right click. A menu of the most common filters is shown; this is much easier than opening up the Filter window.
  • From this window, you can go directly to the help for the given track. There is also a 'Navigation Help', as there are many ways to resize, scroll, etc.
• Sequence track:
  • Show hit score bar is a new filter that shows the hits down the length of the sequence as a histogram showing how strong each hit is.
  • Show Hit Score Value is a new filter that shows the %identity. Note that the sequence graphic is twice as wide to show the score bar and score value.
  • The sequence track can be scrolled by moving the mouse wheel when the mouse is position over the sequence track. This retains the same zoom and filters, but moves up or down the lenght of the sequence (i.e. pseudomolecule).
  • The gene annotation now shows the intron/exon structure.
• Hit track:
  • Show Only Gene Hits (contained) is a new filter that turns off the display of all hits unless they are contained in an annotated gene.
  • Show Only Gene Hits (overlap) is a new filter that turns off the display of all hits unless they overlap an annotated gene (but is not contained in a gene).
  • Show Only Non-Gene is a new filter that turns off the display of all hits unless they are NOT overlapping or contained in a gene.
  • Hit lines are highlighted in red when mouse positioned over a hit.
• Block track:
  • When hovering over a contig, the contig information at the bottom of the display includes all the chromosomes that the contig hits.
• Distributable:
  • Improved console error reporting for bad input parameters during installation.
  • Improved help and trouble shooting section.
• Bug Fixes:
  • Genes drawn incorrectly when sequence range within gene boundary.
    
  • Fixed bug with pseudomolecule filter.
    
  • Certain queries were failing when used with MySQL 5.0.26 due to comma precedence change.
    

New Features in Back-End Processing (Perl scripts):

• Support for mixed letter/number chromosome names and arbitrary ordering (see example in demo-fpc params file)
• Pseudomolecule sequences loaded in 1Mb chunks, removing database problems with large text fields
• Filtering optimized in anchors.pl to reduce memory use in loading large blat outputs

Version 1.0

Release date: 9/1/06
First full public release.

Known Issues:
The FPC/FPC mapping mode of this release is known to have problems with MySQL 5.0.26, and possibly earlier releases.

Note: the algorithm and systems are as described in
C. Soderlund, W. Nelson, A. Shoemaker and A. Paterson (2006)
SyMAP:A system for discovering and viewing syntenic regions of FPC maps.
Genome Research 16:1159-1168.