Download ONLY primary transcripts from plants

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5.0 years ago

aboutmb • 0

Hi, everyone!

I study flowering plants and I need to download only primary transcripts from them. So I've been using Phytozome for this purpose. But I'ld like to work with as many as possible species and Phytozome has restricted number of species.

So, does anyone know anyway to obtain accurate primary transcripts besides Phytozome?

Thank you so much!

primary transcripts plant phytozome ensembl ncbi • 1.1k views

ADD COMMENT • link updated 4.9 years ago by Biostar 20 • written 5.0 years ago by aboutmb • 0

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PLAZA

comprehensive list of species but not exhaustive either

ADD REPLY • link 5.0 years ago by lieven.sterck 15k

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Check Ensembl plants.

ADD REPLY • link 5.0 years ago by GenoMax 141k

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I've checked, but Ensembl hasn't only primary transcripts. I've compared Ensembl and Phytozome for some species and I got different number of sequences.

Thank you anyway!

ADD REPLY • link 5.0 years ago by aboutmb • 0

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No site is likely to list primary transcripts alone since that is a concept subject to change/interpretation. What is your criteria for calling something a primary transcript? That it be the longest and/or most abundant?

Number of isoforms you are going to see is going to be different for each site based on their method of annotation/evidence being used for that annotation.

ADD REPLY • link 5.0 years ago by GenoMax 141k

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