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SyMAP v2.0 User Guide
Last update: 8/31/07This guide describes the SyMAP web interface that provides a gateway to the SyMAP applet. For help with the SyMAP applet, run the applet and click the "?" help button.
1 Overview and System Requirements
SyMAP analyzes alignment data between FPC maps and pseudomolecules or other FPC maps. The raw input data consists of individual alignments, or "anchors", for example sequence alignments of BAC-end sequences to pseudomolecules. From the anchors, the system determines regions of alignments known as "synteny blocks". The blocks consists of one or more contigs which align to contiguous regions on the pseudomolecule (or other FPC map). For further details on how the alignments are computed, see the SyMAP publication (reference on main page). The remainder of this document is devoted to the SyMAP display system.The SyMAP display system has two components:
- HTML/CGI web pages
- Java applet
To view these pages requires only a web browser.
The Java applet provides detailed views of the alignments, in which all evidence
may be fully examined. The Java applet also provides a dot-plot view.
The Java displays require Java Runtime Environment v1.5 or later.
The first section gives options for FPC maps aligned to a pseudomolecule (rice
in this case), while the second section provides similar options for alignments
of FPC maps to FPC maps.
The options in the first two sections are as follows:
The final section leads to "dual alignments".
The full-genome block view (below) shows all the synteny blocks found by SyMAP, and
their alignment locations along the pseudomolecules. The blocks are color-coded according
to their chromosome (as given by framework information in FPC).
Blocks of unanchored contigs are also shown, with the color black.
Unanchored contigs may or may not be close to one another in reality, but they are joined for
display based on the proximity of their alignments on the pseudomolecules.
Clicking on one of the pseudmolecule bars leads to the
single-chromosome block view.
This view shows the blocks found to align to a particular chromosome.
Individual contigs making up the blocks are labeled.
Green lines indicate the region of the alignment along the pseudomolecule,
and they are crossed if the alignment is inverted.
Clicking on one of the blocks runs the SyMAP applet to show a detailed display
of the alignment.
The "Compare Blocks" section allows a 3-track alignment to be set up, having one block
on the left and one on the right (see discussion of dual alignments).
This view shows the alignment locations for each contig separately, along with data columns
The contig numbers are links leading to Java displays of the particular alignment.
Above the table are two link options. The first shows contigs aligning to multiple locations,
which is useful as these contigs may contain rearrangement breakpoints, or may be chimeric.
The second shows contigs with no alignments.
If the FPC project contains clone remarks, the alignments in the table may be filtered
on them, using the "Show only contigs containing this remark" option.
At the very top is an option to show all contigs aligning to a given chromosome.
They are shown in the Java viewer, arranged in the order of their locations on
the pseudomolecules.
(Note that the table view described here is for FPC/pseudomolecule alignments; for FPC/FPC
alignments, it lists only aligning contig pairs and their scores).
These options permit 3-track alignments to be set up, showing two different
synteny blocks aligned on either side of the pseudomolecule they align to,
as shown in this
example.
Dual alignments are shown in the Java applet, and the left and right blocks
need not come from the same species.
Detailed description of the applet is available through its help menus.
2 Description of HTML and CGI web displays
The HTML/CGI display set comprises the following types of pages
Projects Page
Below is the Projects Page as it appears on the AGCoL site.
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Full-genome block view
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Single-chromosome block view
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Contig alignment table
as follows:
Contig the contig number
#Clones number of clones in the contig
CB size size of the contig, in consensus band (CB) units1
Chr pseudmolecule chromosme the contig aligns to
Score number of anchors supporting the alignment
Start,End start and end location, in basepairs, along the pseudomolecule
Comment at present, this field gives the average %identity of the anchor
alignments for marker and BES, respectively
All columns may be sorted using the up/down arrows in the header row. 
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Dual alignment selector
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1Contig size in FPC is measured in CB units; for details, see
Soderlund, C., I. Longden and R. Mott (1997) FPC: a system for building contigs
from restriction fingerprinted clones. CABIOS, 13: 523-535. Download
