How I can find flanking regions

Question

[hosin]

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

[Sishuo Wang]

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

[WouterDeCoster]

How I can find flanking regions for them.

You should elaborate what that means for you.

[Denise CS]

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.

[hosin]

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?

[WouterDeCoster]

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

[hosin]

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

Answer 1

[Tm]

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.