SyMAP 4.0 Tour  
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Following is a quick tour of the many displays and features available through SyMAP.
For more information see our plant syntenies and the System Guide.

Contents

High-level browsing:
  • Explorer
  • Dot Plot
  • Dynamic Circular View
  • 3D View
  • Block View
  • 3-Species Figure
  • Detailed views:
  • Side-by-side View
  • Closeup
  • Base View
  • Analysis:
  • Query Setup
  • Query Result
  • Gene Families
  • Multiple Alignment
  • Management/Web:
  • Project Manager
  • Web Interface
  • Chromosome Explorer

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    The Chromosome Explorer allows you to select multiple chromosomes from different species and view their alignment using several views: 3D (shown here); dot-plot; circular; and side-by-side.

    Chromosomes, and a reference chromosome, are selected through the lefthand panel, and the desired alignment view is shown to the right. Below is an example showing three chromosomes from Maize, Rice, and Sorghum against Maize chromosome 9.

    The 3D view, shown here, is available in the standalone Java application (not over the web). It shows a three-dimensional display of the syntenic regions ("synteny blocks") for selected chromosomes against the reference chromosome. Inverted blocks are shown in green.

    Dot Plot

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    The multi-species dot plot shows the selected chromosomes aligned against the reference (top axis). Here Maize chromosomes 6 and 8, and Sorghum chromosomes 3 and 9, are aligned against Rice chromosome 1, clearly showing the pattern of duplications. Synteny blocks are outlined in blue, and one can click to zoom further and arrive at a more detailed side-by-side display.

    Circular View

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    The Dynamic Circular display shows a circular view of the synteny blocks between selected chromosomes. (The method of selecting chromosomes is the same as for the 3D view.) Below is an example for Rice against Sorghum.

    This is the initial display when launching the Java Explorer through the web. (The web displays also include a static version of the circular display which shows all chromosomes for a single pair of species.)

    Block View

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    The Block View shows a chromosome-level view of the synteny blocks for one organism aligned against the chromosomes of another organism. It is available both through the web and in the standalone Java application. Below is an example for Sorghum against Rice.

    The synteny blocks are colored by chromosome (see color key at top) and clicking on a chromosome track leads to the single-chromosome view shown below:

    This view shows the individual synteny blocks in more detail; clicking on a block leads to the side-by-side display.

    Side-By-Side View

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    The Side-by-side view shows regions of two chromosomes aligned as below. This view allows access to full details of the alignment, including each individual anchor and annotation.

    Each individual anchor point (a.k.a. "hit", generated by MUMmer or BLAT) is shown as a brown line between chromosomes. Zooming in further one can see the exon-level annotation, with yellow description box, and the detailed anchors connecting these genes.

    It is possible to zoom in even further and see a basepair-level view of the region, with Needleman-Wunsch alignments generated on the fly:

    Query Interface

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    SyMAP v4.0 includes powerful search features to help make the most of synteny information. Aligned regions across the selected species are automatically grouped into "putative gene families". The filters allow you to locate the families of interest based on annotation, level of synteny, and presence or absence in different lineages.

    Query Results

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    The query results table has full flexibility in column selection, column ordering, and save/reload of searches. For example if you find an interesting family that is not annotated, you can easily save all the relevant sequences as a fasta file for further study.

    Gene Families

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    The hits are grouped into gene families.
    The PgeneF number is a unique number assigned to the gene family.
    The PgFSize number is how many unique instances are in the family.
    The #RGN tells how many times the gene occurs for the species.
    Example: For PgeneF=1 of PgFSize=2, Medicago #RGN=1 and its two Start coordinates are about the same, whereas Soybean #RGN=2 and its Start coordinates are on different chromosomes.

    Multiple alignment

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    Another unique option is to send the selected sequences directly to Muscle for multiple alignment, to reveal the patterns in the sequence alignments between the species. SyMAP parses and displays the MUSCLE (Edgar 2004 NAR:32) results:

    Project Manager

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    A full-featured manager enables the creation, alignment, update, and viewing of any number of species projects with only a single external configuration file giving database information:

    Web Interface

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    All SyMAP displays with the exception of 3D are accessible through the web. A basic interface is provided (shown below) and this is easily customizable (e.g., example).

    Overview Figure Script

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    The provided script 3track_figure.pl generates a 3-species synteny overview at resolution suitable for publication. The script is customized by editing the species names and database information at the top, and the colors are also easily changeable. (Modeled on script provided by Shifeng Cheng (BGI); requires perl CPAN packages SVG and Data::Dumper).