See Terminology in the User Guide, especially the Cluster Hit Algo1 versus Algo2 description.

>Instructions

The Instructions window (above) lists the projects which were selected for querying. The last line states what the Olap column represents; if one or more project pairs used Algo1, it will be gene overlap; if all project pairs used Algo2, it will be exon overlap

Open the Query Setup window by clicking on its tab in the left panel.

Set up the desired filters and then select Run Search to execute it. When the query is complete, the query result panel will be displayed.

Rules

1. All queries are on the Pair hits unless Single is selected. 2. All Pair hits queries return a row per hit pair, i.e. aligned region between to two chromosomes from two projects. 3. Major and Minor genes: A hit can align to multiple genes on either or both chromosomes; it is assigned to the best (major) gene on each end. For example, in the image on the right, the red highlighted gene is the major gene for the highlighted hit, whereas the purple single exon gene is the minor gene. When queries involve genes, only the hits to the major genes will be shown except for the following queries, which will also list the minor genes:    Annotation, Every*, Hit#, Gene# when no suffix is provided, and Multi with minor checked. 4. Most filters can be used in conjunction with other filters; options will be disabled if they cannot be used with a selected filter.

Location

It is valid to only enter the From or To, or no value for either (leave blank).

• Orphan genes (no hits)
  Genes that do not a have a hit and meet the additional filters. The orphan genes are relative to the projects shown on the Instruction page. For example, if species X, Y and Z have synteny computed between all pairs, but only X and Y are selected, the orphan genes for X would be those with no hits to Y. If X,Y&Z are selected, the orphan genes for X would be those with no hits to Y and Z.
   
• All genes (w/o hits), i.e. genes with and without hits
  This shows all genes that meet the additional filters, regardless if they have a hit or not. There is always the same set of genes for a project, regardless of synteny.

Allowed filters for singles: both options can be restricted by:

• Using the Project pull-down, select a project.
• If a project is selected, then a chromosome and optional location can be selected.
• An Annotation Description may be entered.

In Block (Synteny Hit)

Annotated (Gene Hit)

Collinear size >= N (or = N or <= N)
List all hits in collinear sets that have size >= N. See Collinear, which explains the SyMAP collinear sets.

Multi >= N
List all hits that align to genes on at least one end with >= N hits. Check Minor* to include minor hits.
When used with a specified chromosome, restricts genes >= N hits on the specified chromosome; see Rules for genes/chr.

Block#
Enter a single block number (the Block column is formatted Chr.Chr.Block#). Use it in conjunction with the chromosome pull-downs. For example, if you select Chr 1 from the first project, Chr 2 from a second project, and enter block=3, you will see hits in block 1.2.3 from the two project chromosomes you selected.

Collinear Set#
Enter a set number (the Collinear column is formatted Chr.Chr.Size.Set#). All hits in a collinear set have the same Set#, which is the last number of the Collinear column. This can be used in conjunction with the chromosome pull-downs (as for blocks).

Hit#
The hits are numbered for each chromosome pair, e.g. there will be a Hit#1 for every chromosome pair that has hits. If a hit aligns to multiple genes, both major and minor genes will be shown.

Gene#
Enter a Gene# number (the Gene# column is formatted Chr.Gene#.suffix where the suffix may be blank); do not include the 'Chr' number.
 • If only a number is entered, all genes with the numeric prefix will be displayed (including minor hits).
 • If a number.suffix is entered, the exact gene will be displayed (but no minor hits).
 • See Rules for genes/chr

Rules for genes/chromosome queries: The following queries involve genes and how they respond to a specified Chromosome. All queries first filter on location, but only a "Yes" further restricts the genes to the selected chromosome(s).

This is only computed if the Computed PgeneF is checked. Using the hits that pass the other filters, SyMAP constructs putative gene families (PgeneFs) spanning the selected species. This is done by grouping hits which overlap on at least one genome. Note, if you have more than 6 species selected, this stage can take an hour or more.

Each PgeneF is given a number, which is shown in the Query Results table (column name PgeneF). The size of the PgeneF is also shown (column PgFSize).

Filters using the PgeneF values:

Include/Exclude
These filters permit searching for gene families shared by one group of species but not present in another.

If a species is checked to include, then the PgeneF will only be retained if it includes at least one hit which hits that species.

For >2 species only: If a species is checked to exclude, then the PgeneF will be discarded if any of its hits are to that species.

For the included species:

1. Results Table

• Pair Hits:
  • The table contains columns for all of the selected species, but each hit only connects two species, and the other species columns are empty.
  • Each Hit# is only listed once unless minor genes are included (see Rules).
  • A gene may be listed more than once if multiple hits align to it with a best overlap (i.e. major gene with multiple hits).

• Single genes:
  • If the query specified Single genes, then each row represents one gene and shows data only for one species.

You can sort the columns by clicking the column name in the table, and rearrange them by dragging the column name. You can add/remove columns using the Select Columns button at the bottom.

The buttons on the bottom will be Select Columns and Hide Stats. If Select Columns is selected, it changes to Hide Columns and the Hide Stats is replaced with Clear and Defaults.

In the column panel shown above, hover over a column name to see its brief description. Following are the full descriptions of the columns.

Single result from 3 selected species

Single result from 2 selected species

In the above tables, the A.thal gene #2 is the 2-species table because it has not hit to Cabbage; but it is not in the 3-species table because it does have a hit to A.thal. The values of NumHits is the same in both. That is, they both are showing orphan genes relative to the selected set, but the NumHits lets the user know if its orphan over all the computed sets.

The other query on singles is for All genes, which provides the same columns.

2.3 Auto-save columns

Say the last database D_n queried had N species, and the current database D_m has M species, where D_n and D_m are different SyMAP databases:

1. If N=M: the General and Gene&Hit Info columns will be set according to the previous settings, but the Annotation columns may be wrong.
2. If N>M or N<M: the General will be according to the previous settings, all Gene&Hit Info columns will be set like the first D_n species, and no Annotation columns will be set.

Show: For the selected row, a popup will show all columns and associated information for the hit. The text in the popup can be copied.

Align: Select one or more rows. The sequences of the selected hit(s) are written out and a multiple alignment is created using MUSCLE (Edgar 2004 NAR:32). The figure on the right shows the MUSCLE alignment of two genes from B.rapa and genes from Cabbage and A.thal.

Region (kb) The selected hit is padded to each side by the amount indicated (default 50kb). The default filter is Show all hits. Synteny block The entire block for this hit will be shown. The default filter is Show Block Hits. Collinear set If the hit is in a collinear set, the set will be shown. The default filter is Highlight Collinear Set; Show Block and Set Hits.

High: If this is selected, the selected hit is highlighted in red; the selected color is the same as the hover color, and can be changed in the Color Icon.

Export: One or more rows can be selected for the following exports; or if no rows are selected, the entire table is exported.

CSV: Export the rows using the selected set of columns to a CSV format suitable for import into Excel. HTML: Export the rows using the selected set of columns to a HTML format suitable for viewing on the web (e.g. Example). FASTA: (Pairs Only) Sequences from the rows are written to a FASTA file. Both sides of each hit are written using the start/end coordinates shown in the table. NOTE: this is a very slow function and takes minutes if many rows are selected.

Most of the statistics are self-explanatory except the following:

Annotated and Genes: The first is the number of hits that overlap one or more genes, where a gene can have multiple hits. The second is the number of Genes with at least one hit.

Regions: This statistic is only shown if Compute PgeneF was checked, and it is the number of distinct regions covered on that species.

All query results are listed under the >Results tab on the left. Clicking this tab shows the table of queries illustrated above. Query results can be displayed by clicking a result on the left panel, or double-clicking it in the list of results table shown above.

The only way to remove query results from the left tab is by selecting them in this table followed by Remove Selected Query.