Question: How I can find flanking regions
0
gravatar for hosein_salehi6
10 weeks ago by
hosein_salehi60 wrote:

I have sequences of some coordinates ( like: chr24:40902129-41709809, chr25:11035146-11097889) from oar_v4.0_27.fa file. How I can find flanking regions for them. Thanks

sequence • 250 views
ADD COMMENTlink modified 10 weeks ago by toralmanvar530 • written 10 weeks ago by hosein_salehi60

Hi, You may feel bedtools flank (link) helpful,

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Sishuo Wang140

How I can find flanking regions for them.

You should elaborate what that means for you.

ADD REPLYlink written 10 weeks ago by WouterDeCoster32k

Flanking region is any sequence that is next to any site in the genome, either side, up or downstream. You can choose how much flanking sequence you want depending on what you want to do with this information (e.g. design primers for PCR, carry out sequence alignments for closely related species versus distant related species).

Depending on how much coding you do or how many sequences you want the adjacent (flanking) regions for, you can use a genome browser such as Ensembl and export the sequence by choosing how many nucleotides up (5') and downstream (3') you want.

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ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Denise - Open Targets4.6k

Actually I want to design primers for QPCR, for some coordinates ( like: chr24:40902129-41709809, chr25:11035146-11097889 ). So ,the QPCR primers should be on the flanking , that is non-repetitive sequence inside . How can I select this regions?

ADD REPLYlink written 10 weeks ago by hosein_salehi60

It's always useful to mention things like that from the beginning.

ADD REPLYlink written 10 weeks ago by WouterDeCoster32k

How about Oar_v4.0? , because I think your offer is for Oar_v3.1 in Ensembl

ADD REPLYlink written 10 weeks ago by hosein_salehi60
1
gravatar for toralmanvar
10 weeks ago by
toralmanvar530
toralmanvar530 wrote:

You can use seqkit subseq with -d (for downstream seq) and -u (for upstream sequence) option or "--only-flank" option to get only up/down stream sequence based on your requirement.

ADD COMMENTlink written 10 weeks ago by toralmanvar530
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