Compare Smed assemblies
Welcome to PlanMine, an integrated web resource of data & tools to mine Planarian biology.
If you are short of time, just navigate through our set of quick tips on general utility and specific features. For a basic overview of the site and its features try the User Guide, it takes about ten minutes.
In the top right hand corner of every page you will find the PlanMine Search Box.
When search results are displayed you can also filter results based on category (e.g. Contig, Interpro Domian, Other Protein Domain, TreeFam, GO Term) (See example to the left). It is also possible to filter by organism and assembly (for species with more than one assembly). When results are filtered by category you can also save the results as a list for further use.
Our integrated BLAST search page allows you to search against all contigs stored in PlanMine with a query sequence of your choice. You can search against all assemblies or just select those you wish. Advanced BLAST parameters are also supported for search customization. Blast funcitonality is provided through the integration of the SequenceServer tool.
See the Blast section in our user manual for more information searching using a query sequence.
Lists allow you to manipulate sets of data at once. It is possible to upload your own lists of favourite contigs and save lists from results tables produced by searches. We have also created useful public lists that may be of general interest.
You can use the lists tab to:
See the lists section in our user manual for more information on generating and working with lists.
Templates provide predefined quick access to many of the useful search functions of planmine. We have preconfigured a number of forms allowing you to simply paste your input data (keyword, id, list) and query the database using various filters to give a results table.
Templates cover questions such as:
For advanced searches the QueryBuilder tool is very powerful and for help with this see the section in our user manual.
Mymine is the place to store your own personal
The MyMine tab at the top of the page in the place to go for this functionality, but first you must create an account with use by providing and email address and password.
The Species Pages provide background information on each species represented in PlanMine with a transcriptome. Information includes
You can browse and access the species pages via the picture links on the home page.
For each Smed transcript, the transcript pages give information on
Differential gene expression data is currently only available for the dd_Smed assembly, utilizing published data sets. Access the transcript page by querying a specific transcript ID or clicking a transcript ID in a BLAST search results page.
No de novo assembled transcriptome is perfect. Transcript comparisons amongst the 5 independent Smed assemblies in PlanMine allow you to:
Planarians rely on abundant adult pluripotent stem cells to continuously renew all organismal cell types. PlanMine therefore offers a unique phylogenetic perspective on stem cell pluripotency. Salient features include:
Planarians are situated in a scarcely sampled corner of the tree of life. The planarian transcriptomes in PlanMine therefore provide a strategic resource for studying gene evolution. Useful features include:
Compare Smed Assemblies
Compare Smed assemblies
Compare any other assemblies
Search contig functions
Find more information for contigs
To cite PlanMine, please refer to the following publication:
Brandl, H., Moon, H., Vila-Farré, M., Liu, S.-Y., Henry, I., & Rink, J. C.