REPETDB
REPETDB is a database of transposable elements. Reference sequences for various species are stored with the Intermine data warehouse framework.
Reference transposable elements are presented with their evidences allowing to determine their classification according to PASTEC , the classifier of the REPET package. Transposable elements can be queried and visualized using the powerful capabilities of Intermine .
Most of the REPETDB datasets also provide the consensus copy annotation on genome via a Track Hub referenced on Track Hub Registry .
Refer to the documentation for more information about the REPETDB data submission.
Refer to use cases for using RepetDB
- Get fasta sequence of a set of consensus : RepetDB_Get_consensus_fasta_seq_from_list.pdf (5.71 MB)
- Create and manage list : example of list of consensus matching with HMM domain profile : RepetDB_UseCase_ConsDomain_createAndManageList.pdf (10.06 MB)
- Search copies of TE consensuses located on a genomic region : RepetDB_UseCase_Search_copy_in_genomic_region.pdf (17.67 MB)
Blast sequence against RepetDB consensus database
- Select the "Repeats" group
- All the results have 2 links
- download the matching consensus sequence
- Link to the matching consensus card in RepetDB
RepetDB citation
Creation date: 02 Jun 2017
eZ PublishPublication supervisor: A-F. Adam-Blondon
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