Definitions :

- Conserved segments (CS):

Region containing markers/anchors (that belong to the same chromosomes) contiguous between 2 genomes and that may have alterations in gene ordering. (See also Output interpretation)

- Conserved segments Ordered (CSO):

Region containing markers/anchors contiguous between 2 genomes without alteration of order or orientation. (See also Output interpretation)

- Breakpoint:

Limits between 2 CSs and/or 2 CSOs. (See also Output interpretation)

- Adjacency Penalty:

It correponds to a number of genes/markers (on the tested chromosome) set by users that makes an interruption in the colinearity of a Conserved Segment.
All genes of a species have precise locations and are consequently (pre)ordered within genomes. AutoGRAPH algorithm tests the difference of order for 2 adjacent markers on tested chromosome.
It permits to identify CSO(s) in a CS.
For examples: it allows user to identify:
a) Inversion
If we have respectively these orders of anchors (orthologous genes) in 2 species:

On reference species: 1 2 3 4 5 6 7 8 9 10
On tested species: 1 2 3 4 5 10 9 8 7 6
AutoGRAPH adjacency test: 1 1 1 1 1 5 -1 -1 -1 -1
    (2-1) (3-2) (4-3) (5-4) (5-10) (9-10) (8-9) (7-8) (6-7)
An adjacency penalty of 3 identifies 2 CSOs (from 1 to 5 and from 6 to 10) in the CS.

b) An interruption in a CS, that corresponds to 2 CSOs
On reference species: 1 2 3 4 5 6 7 8 9 10 11
On tested species: 1 2 3 7 8 9 10 11 12 13 14
AutoGRAPH adjacency test: 1 1 1 4 1 1 1 1 1 1 1
    (2-1) (3-2) (7-3) (8-7) (9-8) (10-9) (11-10) (12-11) (13-12) (14-13)
In the same way, an adjacency penalty of 3 identifies 2 CSOs (from 1 to 3 and from 4 to 11 on the reference chromosome and from 1 to 3 and from 7 to 14 on the tested chromosome) in the CS.

- Min. number of marker(s) in CS(O) in text results:

Select the minimum number of markers/anchors to define a CS(O) and to be listed.
These informations are stored and displayed in the results array at the bottom of the figure and in a flat file to be downloaded.

- Breakpoint density:

Density in breakpoint regions is defined as a number of marker(s) in a window of 1Mb surronding the midpoint of the breakpoint region on the reference chromosome.

- Singleton:

A singleton is defined as a single gene or marker that identifies the comparable region in a tested genome, but does not cluster with other genes or markers to form a segment.
Singleton are identified by (**) on synteny map (Reference genome) but the tested geneome is not displayed the figure in order to be an easier way to visualize CS(s) and CSO(s).

Questions asked :

- What is the input format for the personal dataset module?

Datasets are flat files containing 3 fields in column tabulated format.
The first field corresponds to the marker/gene identifiers (example: BRCA, ENSCAFG00000006289...).
The second is the chromosome attribution (example: hsa21, 21 or HSA_21...) : it must be unique for the dataset of reference !
The last field is the localization of the marker/gene on the chromosome(s): it must be an integer in order to apply ordering function.

(See also tutorial)

- Data must pre-ordered to be analyze by AutoGRAPH?

No, AutoGRAPH orders your datasets before constructing synteny map so you don't have to (pre)order your datasets yourself.

- How can I "navigate" on the reference chromosome ?

A javascript application is able to display orthologous informations when mouse is over the chromosome of reference. In preinserted module, a link on ensembl web site is provided for each genes of the reference dataset. (See example ).

- Can I save the comparative map displayed on the ouptut?

Yes, you can save synteny map resulting from AutoGRAPH analyses by click on the links "Save Image" on the left top of the map or by right click on the image and select "save as".

- Do I need to install a java plugin on my computer to use AutoGRAPH?

No, there is no need to install a java console to launch AutoGRAPH. All analysis run on the server and not on the client computer.

- What are the format of map output picture?

Two file formats are available (PNG and JPEG) but we are working to develop other image formats using GD library (gif, bmp...)

- Where can I find public data (preinserted datasets) in convenient text format?

The Ensembl web site provides the Biomart tool to facilitate downloads of gene positions for many species.

- I have some problem to see javascript bullet?

if you use IE 5.0 on a Mac, some dynamic links (mouse-over) may not work.

Dec-07-2023, 18:17Questions/problems logo_dv