Question: How to extract promoter sequences from a plant draft genome?
0
gravatar for Dineshkumar K
8 weeks ago by
Kasaragod, Kerala, India
Dineshkumar K30 wrote:

I would like to extract promoter sequences from a draft plant genome. I found many web tools for the same, but those are accepting small file as a input sequence (maximum 5 mb). I have 350 MB sized plant draft genome, therefore please suggest me any off-line tool for the prediction of promoter sequences. Thanks in advance.

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by Dineshkumar K30
2

I faced the same problem around year ago working with Nicotiana tabacum genome (annotated scaffolds). At that time I did not find the solution so just tried to write my own bash script that utilizes the common software like samtools and bed tools and outputs multi fasta with promoter sequences. Here is it: https://github.com/RimGubaev/extract_promoters Hope this could help!

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by rimgubaev140
2

Looking at that code, it is mainly extracting flanking sites from annotated genes. While this is broadly addressing the goal, this should not be confused with finding bona fide promoter sequences, merely the regions where they would actually be found.

I say this just in case someone in future comes to this thread and runs that code as a 'black box'.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by Joe14k

Yeah, that's correct, thanks!

ADD REPLYlink written 8 weeks ago by rimgubaev140

Thank you @rimgubaev

ADD REPLYlink written 8 weeks ago by Dineshkumar K30

Many thanks, dear colleagues!

ADD REPLYlink written 8 weeks ago by natasha.sernova3.6k

Do you just want 1kb upstream of genes? That's one line of bedtools.

ADD REPLYlink written 8 weeks ago by Asaf6.4k

yes indeed @Asaf, could you please elaborate it.

ADD REPLYlink written 7 weeks ago by Dineshkumar K30

Take a look at bedtools flank

ADD REPLYlink written 7 weeks ago by Asaf6.4k
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