Can Toucan Tool Be Applied To Plant Genes?

Question

[Sunflow]

When I launched the TOUCAN v. 3.0.2, I found it accepts the Ensembl ID (start with ENSG) only, I retrieve the ensembl gene ID of Arabidopsis from here (Gramene):

http://www.gramene.org/biomart/martview/56e6245bdec599856d309fbd1d902125/56e6245bdec599856d309fbd1d902125

and when I load these ensembl ID into the TOUCAN , it fails to retreive the sequences, so I want to ask whether TOUCAN v. 3.0.2 works with plant sequences?

[Neilfws]

Your BioMart URL contains session information which is not persistent, so that link is not useful.

[Neilfws]

Your BioMart URL contains session information which is not persistent, so that link is not useful. Can you supply the ENSG ID instead?

Answer 1

[Brad Chapman]

I don't have direct experience with Toucan, but from the webpage it doesn't look to support plant genomes:

TOUCAN is a workbench for regulatory sequence analysis on metazoan genomes

and the latest version is a few years old:

Version 3.0.2 
Compilation date: May 2007
Supporting Ensembl release: 42

The Arabidopsis cis-regulatory element database is a useful resource.

and TAIR maintains a list of other regulatory element resources: http://www.arabidopsis.org/portals/genAnnotation/genome_annotation_tools/cis_element.jsp

Answer 2

[Stein Aerts]

Sequence retrieval only works on Ensembl, not on Gramene. So automatic retrieval of sequences is not possible for Arabidopsis.

You can use BioMart on Gramene (http://dev.gramene.org/biomart/martview) to retrieve promoter sequences, save them as FASTA, and import them into Toucan (using File-LoadSeq). From then on, all Toucan functionalities are available, such as sequence comparison, motif discovery, PWM matching, PWM over-representation, module searching. These methods are independent on the species, as long as you use the appropriate background models.