Question

Plant Transcript Assemblies

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13.5 years ago

User 7267 ▴ 30

Hai All,

Do anyone know others transcript assemblies database for plants just like PLant TA database (http://plantta.jcvi.org/). Well, I'm looking for database updated for plant transcriptomic but it seems that the database in Plant TA is not updated since 2007.

Thanks!

database plant transcript assembly clustering • 3.3k views

ADD COMMENT • link updated 13.5 years ago by Neilfws 49k • written 13.5 years ago by User 7267 ▴ 30

score 3 · Answer 1 · 2010-10-13

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13.5 years ago

Mary 11k

http://www.plantgdb.org/prj/ESTCluster/

http://www.phytozome.net/maize.php as one example, but there are other species too.

http://solgenomics.net/

There are also a bunch of individual plant sites too.

ADD COMMENT • link 13.5 years ago by Mary 11k

score 3 · Answer 2 · 2010-10-13

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13.5 years ago

Fred Fleche 4.3k

[?]

http://compbio.dfci.harvard.edu/tgi/plant.html

[?]

http://www.ncbi.nlm.nih.gov/genomes/PLANTS/PlantList.html

ADD COMMENT • link 13.5 years ago by Fred Fleche 4.3k

score 2 · Answer 3 · 2010-10-14

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13.5 years ago

Khader Shameer 18k

Have you tried Ensembl Plants ? Ensembl records detailed transcript information in their databases. As of now 8 plant genomes are available via Ensembl Plants.

ADD COMMENT • link 13.5 years ago by Khader Shameer 18k

score 2 · Answer 4 · 2010-10-14

For those who might like to create their own transcript assembly database, the main tool used is TGI Clustering Tools. It is available here, along with some other useful software packages.

Based on the information about TIGR Plant Transcript assembly, I think it should be relatively straightforward to reproduce something similar, from an EST collection of your choice.