Find an uniqe sequence in a range of chromosome coordinates

[thedamian]

Hi All,

I have a range of chromosome coordinates i.e.

HERC6 4:89,280,000-89,350,000

From this range, I have to pull out a subsequence of 200-400 nucleotides. The subsequence shouldn't appear in another part of the human genome. This should be an unique sequence. (The best case, the subsequence would be an exon of HERC6, but not necessary)

Do you have any idae how to automate this process? Which tools/services should I use?


I know I can do this in such way:

Ensembl -> type in the search box "4:89,280,000-89,350,000" -> export data -> cut a subsequence -> paste to the blast.
But this way is not satisfactory.

[Richard Finney]

Just use mabability tracks at CGWB or UCSC ...

No need to brute force this when many folks have done the work already.

Just use any of the mapability tracks available at UCSC or CGWB:

See CBIIT Mapability track at CGWB:

https://cgwb.nci.nih.gov/cgi-bin/hgTracks?db=hg19&position=chr4:89280000-89350000&Mapability=full

Note top track is based on 100bp. Set your window to 200 bp and look for all white in the Mapability track.

There's similar mapability tracks at UCSC :

[dariober]

Hi All,

From this range, I have to pull out a subsequence of 200-400 nucleotides. The subsequence shouldn't appear in another part of the human genome. This should be an unique sequence. (The best case, the subsequence would be an exon of HERC6, but not necessary)

Do you have any idae how to automate this process? Which tools/services should I use?

Hello,

I think vmatch can do what you want, it's a very flexible tool. In particular look at examples 9.9.1 and 9.9.5 of the manual

All the best
Dario