Question: Bulk download tomato RNA or cDNA sequences (partial) with genomic loci list
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gravatar for donger1103
17 months ago by
donger110310
United States
donger110310 wrote:

I have a tomato genomic loci list, such as "SL2.50ch01:89425896-89429084", the locis mostly are inside the exons of genes,but some may also within introns or intergenic spacer. I want to perform miRNA target search, so i need to download all the corresponding partial RNA or cDNA sequences first. are there any tools or ideas? many thanks!

ADD COMMENTlink modified 17 months ago • written 17 months ago by donger110310
1

Do you want to extract the exact ranges as you give an example for or do you want to first look up those locations, then determine in which gene they reside and then extract the (whole) corresponding gene?

ADD REPLYlink written 17 months ago by lieven.sterck5.5k

to lieven.sterck, thanks for your reply, i want to extract the sequences (RNA or cDNA, not genomic DNA) of the exact ranges in my loci list, they are partial sequences of genes. thanks a lot. i reply your question here becuase there is no respond when i click "ADD REPLY".

ADD REPLYlink written 17 months ago by donger110310

OK, but the coordinates you are talking about are genomic, right? so you just want to extract that range or do you want to link them to the most close-by genic feature?

ADD REPLYlink written 17 months ago by lieven.sterck5.5k

to lieven.sterck,thanks again. you are right, the coordinates in my list are genomic, and i just want to extract that range (corresponding RNA or cDNA sequence),besides, it would be better if gene annotation is added. Actually, the coordinates i mentioned are the loci of some circular RNAs, i want to perform the circular RNA-miRNA-mRNA interaction, and my first step is to extract the specific sequences of the circular RNAs and then predict the tomato miRNA targets with tools like psRNATarget. Do you have any ideas? thanks :)

ADD REPLYlink written 17 months ago by donger110310

OK, I would get the genomic fasta files local, build a blastDB from them and then extract all the ranges you want with the blastdbcmd cmdline. Not that difficult to loop over your list and select each region. that will give you already all the genomic sequences, to get the corresponding gene annotation might be a bit more cumbersome but you might be able to do that with BED intersect or so.

ADD REPLYlink written 17 months ago by lieven.sterck5.5k

Thanks you so much, however, i still get the genomic sequences ,not the RNA sequences, right?

ADD REPLYlink written 17 months ago by donger110310

You will get genomic sequence corresponding to the coordinates of loci you are interested in. You have said above that they are not necessarily all in coding regions.

ADD REPLYlink written 17 months ago by genomax70k
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