Question: Howto Find Telomeric Regions In Ngs Assembly
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gravatar for Leszek
8.8 years ago by
Leszek4.0k
IIMCB, Poland
Leszek4.0k wrote:

Do you have an idea how to get subtelomeric and telomeric regions of the newly sequenced organism? I have got fungal species assembly with >50x coverage and closely related genomes already sequenced.

Cheers,

assembly next-gen sequencing • 2.0k views
ADD COMMENTlink written 8.8 years ago by Leszek4.0k
1
gravatar for Michael Dondrup
8.3 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

Telomeric regions consists of highly repetitive chunks of sequence, they shouldn't be in the assembly after all, but try RepeatMasker or Dust to detect such low-complexity regions in the assembly.

ADD COMMENTlink written 8.3 years ago by Michael Dondrup47k
0
gravatar for Stevelor
8.4 years ago by
Stevelor310
Stevelor310 wrote:

I read a paper about synteny...they also talk about assembly of related genomes and transciptomes....maybe this helps to compare your newly sequenced organism with the related ones by their synteny..?? just an idea....

Have a look: http://genomebiology.com/2011/12/5/R45

Cheers Steve

ADD COMMENTlink written 8.4 years ago by Stevelor310

Sorry, but syntheny has nothing to do with telomeres (telomeres always located at the 'ends' of the chromosme), just throwing in some random answers?

ADD REPLYlink written 8.3 years ago by Michael Dondrup47k

In some cases if the organism are closely related their is syntheny of genes, also of genes which are nearly located to telomeric regions....i thought of taking these genes as a marker which might gives you a hint for telomeric regions in their up/downstream regions......

ADD REPLYlink written 8.3 years ago by Stevelor310
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