Question: Plant Transcript Assemblies
3
gravatar for User 7267
8.9 years ago by
User 726730
User 726730 wrote:

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!

ADD COMMENTlink modified 8.9 years ago by Neilfws48k • written 8.9 years ago by User 726730
3
gravatar for Mary
8.9 years ago by
Mary11k
Boston MA area
Mary11k wrote:

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 COMMENTlink written 8.9 years ago by Mary11k
3
gravatar for Fred Fleche
8.9 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

[?]

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

[?]

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

ADD COMMENTlink modified 8.9 years ago • written 8.9 years ago by Fred Fleche4.3k
2
gravatar for Khader Shameer
8.9 years ago by
Manhattan, NY
Khader Shameer18k wrote:

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 COMMENTlink written 8.9 years ago by Khader Shameer18k
2
gravatar for Neilfws
8.9 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 8.9 years ago by Neilfws48k
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