• For detailed information on installation, see the System Guide.
• Please send bug reports and suggestions to symap@agcol.arizona.edu.

Terminology Project Manager Displays for Selected Pair (Two-Genome Views) Circle Display #1 - details of Circle Dot Plot #1 - details of Dot plot Block Display Summary Displays for All Projects (Multi-Genome Views) Chromosome Explorer (Multi-chromosome) Circle Display #2 Dot Plot #2 2D Display View a region Hovers and popups   Hit,  Gene,  Gene-Hit Control panel and navigation Sequence Filter,  Hit Filter Base align   Graphical,  Text,  Alternatives Dot Plot #3 Queries

• Self-synteny • Data Download • Color Wheel, Print and Help (?) Icons    All colors mentioned in this document are the defaults. Details • Collinear Sets • Highlight conserved genes   The Dot Plot and Circle are available from various places. Project Manager Chromosome Explorer   Click on any image in this document to see the closeup.

Citation: The SyMAP User Agreement requires you to cite the following publication if you use SyMAP results in a paper, poster, or presentation.

	C. Soderlund, M. Bomhoff, and W. Nelson (2010)
	SyMAP: A turnkey synteny system with application to plant genomes.
	Nucleic Acids Res 39(10):e68. Link

	Also cite the MUMmer publication: Marcais et al. 2018 or Kurtz et al. 2004

Terminology

The following is more detailed terminology:

   ./viewSymap

All projects in the database will be listed on the left panel. The date beside the project name is when it was loaded. If a [n] follows the date, it is part of n computed syntenies. Selecting projects on the left panel shows them on the right panel. Clicking the View popups a window with the loaded information about the project. A check mark in the Available Syntenies table indicates the pair has computed synteny that can be viewed.

Click on any image in this document to see the closeup.

Displays for Selected Pair

The Circle display shows the chromosomes arranged in a circle, with synteny blocks shown as colored blocks between the chromosomes. The color of a block comes from one of the two chromosomes it connects; for example, in the image below, the A.thal Chr05 color arc is orange and the corresponding blocks are orange.

Project name: Move the mouse close to the project name until the cursor turns to a finger*, then click once. The following will occur: 1. The project name with colored blocks will be in shown in bold italics. 2. The projects colors will be used for the blocks. 3. For example, in the image on the right, A.thal is in italics and all the block are colored with its arc colors; click Cabbage and the block will be colored with its arc colors. *Note: it is much easier to click the project name when the Reverse toggle has been selected. Otherwise, the mouse cursor may not turn to a finger until it is between the arc and the project name. Chromosome color arc: Move the mouse over an arc, followed by: 1. Click once: the blocks from the chromosome will be shown in front. 2. Click twice: Only the blocks of the selected chromosome will be shown. Click again to undo.

Circle Control Panel

First group of buttons:

	Takes the display back to its original display settings, i.e. for all buttons up to the the first "|".
	Increase the circle size.
	Decrease the circle size.
	Rotate the circle clock-wise.
	Rotate the circle counter-clock-wise.
Rotate	Toggle: Rotate the text to face the circle. Un-toggled: As shown in the above image.
	Toggle: Draw the chromosomes proportionately to their actual length in basepairs. Un-toggled: Each species is allocated the same amount of space, e.g. for two species each one gets exactly half the circle.

The popup menu has:

Remaining buttons:

Self-align	(If self-synteny has been computed) When toggled, the self-synteny blocks are shown.
Reverse	(Only available for 2-genome display) When toggled, the reference will be reversed, i.e. the bottom project is shown on top and uses the reference colors (you may need to click the top projects name to use its colors).
	Prints the circle graphics as displayed.
	Displays the online help.
	A popup window of quick help.

Clicking a cell will replace the whole genome view with the Dot Plot for the chromosome pair, as shown below. Within the cell Dot Plot:  • Click a block once and it will turn beige, click it again to view the 2D display of the block .  • Or, use the mouse to define a region, which will put a box around it. Then click the box to view the 2D display.

The following buttons change the size of the display:

	Revert the display back to full genome and its original size.
	Increase the dot plot size.
	Decrease the dot plot size.
	Toggle: Resizes the species displayed on the y-axis according to the current scale of the species displayed on the x-axis. Un-toggled: Each species is allocated the same amount of space.

The following also change the display:

Drop-down	The drop-down menu allows the reference species on the x-axis to be changed.
Filter	See Dot Plot filter below.
	See Color Wheel, Print and Help.

Information buttons:

	Displays the online help.
	Popup of quick help.
	Popup with more detailed statistics, i.e. more detail than shown at the bottom of the display above. This text can be copied. An example popup is as follows: The (%Id=23) is what the filtered percent identity of the hits are, which can be changed in the Hit Filter. For the 3 Annotated columns, the two percentages in parenthesis are the column (Annotated) percent and row (Block Hits) percent.

As soon as a Filter option is changed, it will be reflected on the dotplot. However, no other panel can be accessed until one of the following buttons is clicked, which will close the Filter window. Save Keep the current settings. Cancel Revert back to the settings used when the Filter window was opened. Defaults Reset to the defaults, which are shown in the image on the right.

Show Empty Regions (Not shown in above image) This option is only present if at least one of the genomes displayed has >=20 chromosomes or scaffolds; this is most relevant when one genome is draft sequence, as there can be rows or columns with no blocks. When the option is deselected, it hides rows or columns that do not contain any synteny blocks.

Size of dots

When the dots are all the same size (Scale dot by hit=None and Dot Size=1), they fit inside of their respective block. However, when they are changed to rectangles or their sizes increase, they can overlap the border of their block. This is illustrated on the right, where the filters are set the Length, Dot Size=3. The black and grey dots are non-block hits. Some of the blue block hits are on the border of the block blue box.

Clicking a chromosome displays a window of the chromosome as shown below; the dotted border indicates an inverted block (i.e. the majority of hits are inverted). Clicking a Block displays its 2D view.

Displays for All Projects

The Explorer is a two-panel display in which the left panel is used to select specific chromosomes, while the right panel shows the synteny for the selected chromosomes.

Below is a snapshot of the Explorer showing the Circle, which is the initial view.

Left panel: The left panel controls which species and chromosomes are shown:

• Click a chromosome rectangle to add it to the display in the right panel. Click it again to remove it.
• Click the chromosome number above a chromosome to make it the reference. (The choice of reference sequence does not matter for the Circle view, but it is important for the 2D and Dot Plot views; see below).
• Adding and removing chromosomes affects the Circle view instantly. To add/remove from the 2D or Dot Plot views, open the Circle view, make the change, and then re-open the 2D or Dot Plot.

Informations: As the mouse moves over various components, instructions or information for that component are shown in the Information box.

Views: The buttons in the lower-left corner of the window change the synteny view in the right panel.

Download Blocks: Exports a table of all of the synteny block coordinates for the selected species; see also Data Download.

Click the minus (-) button next to a project name or the Information box, and that section will be hidden; the minus sign will change to a plus. Click the plus (+) button to show the project or Information box.

Right panel: The right panel shows the synteny display for the species and chromosomes selected on the left. The three view for the right panel are Circle, 2D and Dot Plot. The Circle and Dot Plot are essentially overviews, while the 2D view allows zooming down to details, all the way to the basepair level.

Dot Plot #2 (Multi-chromosome)

Full display

Below is an image depicting an alignment from A.thal Chr04 to Cabbage Chr01 to B.rapa Chr02. Note that Cabbage Chr1 is the reference chromosome, hence is placed in between the others.

Each chromosome is drawn as a light-blue rectangle, called tracks. The sequence length is shown at the bottom of a track; the coordinates are displayed on the side. If the sequence has been flipped (i.e. A.thal Chr04), its sequence length is shown at the top of the track.

The gene annotations (if exists) are drawn down the middle of the rectangle in dark-blue (positive strand) and purple (negative strand). Overlapping genes are horizontally staggered. The hits are the lines between tracks, referred to hit-wires, which connect the hit region on each sequence. Hit-wires colored brown align to the same strand on both sequences (i.e. ++,--) and light forest-green align to different strands (i.e. +-, -+). The display colors can be changed using the Color Icon in the upper right of the Control Panel (shown at the top of the 2D display). The tracks and hits can be filtered; see Sequence Filter and Hit Filter.

Annotations: Annotation data of the following types may be loaded into SyMAP and displayed.

Gene annotations: The introns are drawn as thinner black rectangles. The exons are drawn as thicker rectangles, colored dark blue (positive strand) or purple (negative strand). The staggered genes, where one is further out then the other, indicate overlapping genes; they have the same gene# with a different suffix. Hits: The hit-wires connects the aligned regions on the two sequences. The aligned region graphics, located on the track at the end of the hit-wire, extends the length of the hit. Clustered hits are multiple subhits clustered together with gaps in between, where the gaps are represented by a grey area.

Right clicking on a hit-wire or gene popups a window with additional information. The information in a popup can be copied by dragging the mouse over it followed by the copy command. The popup does not go away until the OK button is selected or the SyMAP is exited. Any number of gene popups can be present.

Note: On Linux Ubuntu, the popup information windows will not stay in front, so get hidden behind the Explorer window; they can be moved to the side.

Hit # The number representing the hit for the chromosome pair. gN (N={0,1,2}) XX (X={E,I,n}) Algo1: Hit overlaps no gene (g0), one gene (g1), two genes (g2). Algo2: Hit overlaps two exons (EE), exon-intron (EI), intron-intron (II), exon-intergenic (En), intron-intergenic (In). See Terminology for an explanation of Algo1 versus Algo2. Block # The block number (0 indicates it is not in a block). Inv Indicates that it is part of an inverted block. cN.M (N≥2) It is part of a collinear set of size N; M is the unique set number for the chromosome pair. Subhits=(N≥1) The number of MUMmer hits clustered into one hit, where there may be gaps or overlaps between hits. Id, Sim These values are from the MUMmer file. For Subhits>1, the values are approximate. Cov The largest length/coverage of the two species. Algo1: This is the full length of the clustered hit. Algo2: This is the sum of the merged subhits. L and R This is the coordinates for the hit on the left and right, respectively.

Popup: To view the popup of a hit-wire, right click on it; the hit-wire must be highlighted in red from hovering over it to be clickable. The wire and the major genes (≤2) will be highlighted red as shown on the upper right; the corresponding popup is shown below.

The Hit Information image on the right shows the coordinates of the subhits for the hit shown in the 2D image above. The top part of the popup is the same as the hit information. The "L" and "R" correspond to the 2D left track and right track. If the hits align to a gene at either end, the major gene(s) are stated. The coordinates are relative to the input genome sequences. Both lists are sorted by start coordinate. The subhit columns # in the two table of subhits align to each, e.g. the rows #2 align to each other. The sequence name that is alphabetically lower (e.g. arab<cabb) is numbered 1-N; the opposite sequence is ordered to match the first. Two subhits may overlap (negative gap) on one chromosome but not the other, as shown below. Select the Align Hits to view their textual alignment. See Align.

Selected Cabbage alignment

Selected A.thal alignment

Gene # is a sequential number along the chromosome. If genes overlap, they will have the same number but a different suffix (e.g. a, b,...). #Exon= is the number of exons followed by their summed sizes. The next line (-(7,160,776...) is the location followed by its total length. The following lines (ID, product...) are the annotation provided by the GFF file. The last line (Exon #4) is the exon that the mouse is over.

Popup: To view the popup of the gene description, right-click on the gene in the track; the selected gene will turn cyan. The top text is the same as shown in the gene information. All hits for the gene for the chromosome pair will be listed. In this case, the gene has two hits, where the first is a minor hit to the gene and is not part of a block (if the All hits filter is not on, this hit will not be shown). Algo1: Only has (Gene N%). Algo2: The (Gene N% Exon N%) represent the amount of gene and exon overlapped by the hit, respectively.

The buttons are described in the order found in the control panel image above.

History Event: SyMAP retains a record of the prior views (like a web browser).

• A History Event occurs when the coordinates or tracks have been changed by (1) any of the four middle buttons (-,+,shrink,scale), (2) select a region with the mouse, (3) use the Sequence Filter to change coordinates.
• Any annotation, highlighting, or hit-wire display changes by Sequence or Hit Filter are NOT a history events.
• When a new coordinate change is applied, it becomes the next history event in the list and all previous history events are cleared.
• The first 3 buttons describe below apply to the history events.

	Go back to its original display.
	Go back one history event.
	Go forward one history event.
	Doubles the base pair view region, keeping the same center.
	Shrinks the base pair view region by 50%, keeping the same center.
	The shrink button reduces the space between tracks. This is useful when viewing more than two tracks, e.g see Exp_2D.
	The scale button resizes the tracks so that they are in the same scale (base pairs per pixel) as the reference sequence track in the view. This is a toggle button, so click it again to undo the scale.

• These two buttons assigns a function to the selected region, which is selected by clicking the mouse left button on a location of the chromosome, drag and release.
• The mouse selection will perform the function of the checked button and the selected item from its popup menu.
• The functions are described as follows:

Zoom

Zoom All Tracks Default Zoom into the selected region and all other tracks with hits in the region. If the selection clips part of the hit, the hit-wire will be shown at the top or bottom of the chromosome track. The hit-wire of the clipped hit can be highlighted just like a fully shown hit. This feature was added for release v5.5.0 and also applies to Zoom Selected Track. Zoom Selected Track Zoom into the selected region; all other tracks do not change.

Show

Align (Max 50kb) Default Open the base alignment view for the selected region (see Base Align). There MUST be at least a partial hit in the region to align. Show Seq Options The allows viewing the actual basepair sequence in a track. A sequence must first be selected, then a popup menu will have the options: Hit Show the sequences of the clustered subhits on the positive strand. If the hit is on the negative strand, it will be reverse complemented (RC). Reverse Hit Show the sequences of the subhits on the negative strand. If the hit is on the positive strand, it will be reverse complemented. Full Hit Concatenate and show the sequence from the start of the first cluster hit to the end of the last cluster subhit. Region Show the sequence from the region selected.

The remaining buttons are:

	See Color Wheel, Print and Help.
	Prints the graphics 2D region to an image file (note, this does not include the control bar, etc).
	Displays the online help.
	Popup of quick help.

Mouse navigation:

→ All options in the first 3 sections occur immediately; Coordinates changes occur on Save.
→ Only Coordinates changes are History events.

Highlight Gene popup Highlight the gene when its Gene Popup is displayed. The highlight color can be changed with the Color Wheel. Show Annotation Display of the annotation descriptions along the right side of sequence (see example). NOTE: this only works if you are zoomed in close enough that they can clearly be displayed. Gene# Display the Gene# beside each gene. This is the SyMAP assigned number; see Terminology for more details. Gene delimiter When the zoom is close enough to view the exons, a black line will be drawn over the top end of each gene. This helps delimit genes that do not overlap (so are not staggered), but are close enough to appear one gene (see example below).

The Sequence Filter for the reference track has one extra option, as shown on the right. When it is selected: (1) If there are 2 tracks, this is equivalent to highlighting the Hit =2 genes (see below), but the gene exons of the conserved genes are also highlighted. (2) If there are 3 tracks, the genes conserved across the 3 tracks will be highlighted. The usage of this feature is a little complex, so the section Conserved provides the details.

A subset of the filters are available by right clicking in the empty space of the chromosome rectangle, as shown on the right. During a Chromosome Explorer session, Sequence Filters are reset to defaults between different 2D displays. Highlighting genes summary: Conserved The exons are highlighted. Filter Gene# The exons, introns and gene delimiter are highlighted. Gene popup The exons, introns and gene delimiter are highlighted. Hit popup The exons, introns and gene delimiter are highlighted the same color as the hit-wire color.

Highlight or Show Synteny blocks Hits that are part of a synteny block. Collinear sets Hits that are part of a collinear set. See example below and Details. Hit =2 genes Hits that align to a gene on both sides (g2). Hit =1 genes Hits that align to a gene on one side only (g1). Hit =0 genes Hits that do not align to any gene (g0). Highlight only Hit popup Highlight the hit-wire when its Hit Popup is displayed. If it aligns to gene(s), the major gene will also be highlight. The highlight color can be changed with the Color Wheel. Identity N% Move the slider to view only the hits with >= the specified identity. This works in conjunction with any of the Show options.

When hits belonging to blocks or collinear sets are highlighted, subsequent blocks/sets will have an alternating color relative to one chromosome of the pair, e.g. block 1 hits will be green, block 2 hits will be pink, block 3 hits will be green, etc. A subset of the highlight filters are available by right clicking in the hit white space, as shown on the right. During a Chromosome Explorer session, any Hit Filter settings will remain set between different 2D displays.

The image on the right has the Sequence Filter option of Show Gene Delimiter and the Hit Filter option of Highlight Collinear Hits. Show Gene Delimiter: Note that the 2nd gene on both tracks would blend in with the 3rd if it was not for the black line at the top. Highlight Collinear Hits: The highlighted hit-wires are all part of a collinear set. The 2nd hit-wire is not highlighted because it does not hit a gene pair, so is not part of the collinear set, but it does not disrupt the set since it does not hit an annotated gene.

Graphical Align (from pull-down)

The aligned base view of the clustered subhits will appears in a new window. This view consists of a ruler along the top showing the area of the sequence covered, the hits, and the genes. In the lower text panel, it indicates that has been trimmed.

Subhits
Subhits are displayed as lines, where red horizontal lines are mismatches, forest green is deletion and a downward arrow is insertion. When two hits overlap, one will be shown above the other. Sometimes one appears to overlap another when they do not; this happens due to gaps.

Clicking on a hit line shows its base alignment view in the bottom of the dialog; if the input genome sequence was soft-masked, the masking is retained in the alignment.

Genes
Annotated genes are displayed below the hits. Blue exons are on + strand and burgundy are on the - strand.

Strand for Algo1: Sometimes it is wrong in the Align view. In this image, the A.thal gene is on the negative strand, but its aligned hit is shown on the positive strand. Most of these occurrences have been fixed in v5.4.8, but a few will have slipped through.

Hover over a hit-wire and right click for the information popup shown below. The Align Hit option aligns the hit as shown on the right. Use the Reverse button to view the reverse complement alignment.

Trimmed alignments: SyMAP extracts the sequence between the coordinates provided by MUMmer and aligns the sequence. When the sequences do not align fully, the alignment is trimmed. This is illustrated above for subhit 5, where the Trim 0,13 indicates that 13 bases were trimmed off the end. If you want to view the alignment without trimming, you can run viewSyMAP with the "-a" flag, as shown on the right.

Un-trimmed hit

Another alternative is to find the hit in the Queries, then view the MUSCLE MSA.

• The 2D does not work for a single chromosome compared to itself. However, by going through the dotplot or blocks view, you can click on a self-chromosome block and view it in the 2D view.
• The Queries does not work for self-synteny.

Data Download

• Queries: The results of a query are shown in a table, which can be exported as a CSV or HTML file. The hit sequences can be exported in FASTA format. See Query Export.

• Explorer: Select the species of interest, open the Explorer, and click the Download Blocks button is at the lower left. This exports a table of all the computed synteny block coordinates for all the selected species, including their self-alignments, if those were computed.

  The columns are:
  Species1 Species2 Chr1 Chr2 BlkNum Start1 End1 Start2 End2 #Hits Genes1 %Genes1 Genes2 %Genes2 PearsonR

  The Genes1 column is the number of genes from Species1 in the block and %Genes1 is the percentage of genes that have a hit. The PearsonR is the approximate linearity of the hits in the chain as measured by the Pearson correlation coefficient; a negative PCC is an inverted block.

Print The print icon is for printing the image, which only saves the graphics area (not control buttons). If this does not provide the view you want, use the system "Screen Capture" (all the images in this document were created with screen capture, along with the images in the SyMAP publications).

Help The right icon (?) brings up this web page, typically to the correct section (obviously, there needs to be an internet connection).

Color Wheel This icon opens a menu for customizing colors; the colors changes are saved in a file called .symap_saved_props which resides in the user's home directory. Hence, the changes are preserved between sessions and for different SyMAP databases. In contrast, Filters changes only exist for the duration of the display.

• Click a tab (e.g. Hit) to view the associated colors.
• Click a color box and a color chooser (far right image) will popup that lets you change the color.
• Ok: Instantiate all changes and close the menu.
• Cancel: Cancel any changes and close the menu.
• Default: For the selected tab, changes all colors back to the default colors.

Dot Plot tab:

!Block g0 Non-block hit to 0 genes !Block g1 Non-block hit to 1 gene !Block g2 Non-block hit to 2 genes Block g0 Block hit to 0 genes Block g1 Block hit to 1 gene Block g2 Block hit to 2 genes Block Rect Rectangle around block