I would like to create a local sequence library using the representative sequences from various plant families/genera/species, to blast and identify sequences for my samples. Currently, I'm using the NCBI GenBank database (which is kind of slow sometimes), but would like to explore other options to speed up the process. I would appreciate any suggestions. Thank you!!
Arabidopsis thaliana is a plant model for whole genome analysis. Fragaria vesca (woodland strawberry), tomato, etc
Databases are generally organism specific or marker specific. If you are not sure about those, its easy and simple to use NCBI for blast. Most of the databases are anyway interlinked.
However, if you want to make a local database, so for that ou need to provide more information in your question.
To make NCBI blast faster, there are some filters available. Try them.
Thank you Wiwiek and Abhijeet! I'm specifically looking for rbcL-sequences across various plant families/genera. So far I've seen genome databases but not something like NCBI with a search option. Do you know by the way how I can download a group of sequences for specific gene (not a single sequence) from NCBI ? Thank you!
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