Question

Transcription Factor (TF) sequence extraction +/- 2000 of Arabidopsis thaliana

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9.3 years ago

alpha09 ▴ 10

I have Arabidopsis thaliana transcription factors and I want to extract sequence +/- 2000. Is there any tool OR way to extract quickly?

Kindly tell me the tool name or any website.

I tried different databases of Arabidopsis thaliana.

next-gen genome gene R • 1.8k views

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by alpha09 ▴ 10

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I have Arabidopsis thaliana transcription factors.

In which form do you have them? Do you have list of names? Coordinates? Motifs?

ADD REPLY • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by GouthamAtla 12k

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Yes I have names and motif.

ADD REPLY • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by alpha09 ▴ 10

Ram · Answer 1 · 2015-08-18

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9.3 years ago

UnivStudent ▴ 440

You can find the resource you need using the upstream/downstream sequence tool using TAIR IDs (https://www.arabidopsis.org/tools/bulk/sequences/index.jsp). Same thing using the Phytozome BioMart (which is probably accessible in R)

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by UnivStudent ▴ 440