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Can Toucan Tool Be Applied To Plant Genes?

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?

software plant sequence
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updated by Stein Aerts • Stein Aerts • written by Sunflow • Sunflow

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

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written by Neilfws Neilfws

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

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written by Neilfws Neilfws

2 answers

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

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updated by Ram Ram • written by Brad Chapman Brad Chapman

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.

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written by Stein Aerts • Stein Aerts

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