Question: Fosmid contamination in C. elegans genome?
gravatar for gtrwst9
22 months ago by
gtrwst90 wrote:

In the C. elegans chromosome X (NC_003284.9) is a complete copy of the C. elegans fosmid H05L03 (FO081428.1) at positions 5898291-5912640. I understand fosmids are vectors used to build sequencing libraries, so is this a contamination?

genome • 514 views
ADD COMMENTlink modified 22 months ago by Ahill1.8k • written 22 months ago by gtrwst90
gravatar for Ahill
22 months ago by
United States
Ahill1.8k wrote:

The chromsome X sequence was assembled from genomic DNA fragments that were packaged into fosmids. In this case, your fosmid (FO081428.1) was one of a number of fosmids that were assembled together to form the inferred chromosome X sequence (NC_003284.9). So this is not a contamination - in fact the chr X sequence was literally assembled from many individual fosmid insert sequences. See the contig entry in the chr X genbank record here.

ADD COMMENTlink written 22 months ago by Ahill1.8k

While it is ok for the genomic sequence to match an fosmid sequence entry, if any functional element sequences from fosmid are present in the genome assembly then that is contamination. gtrwst9 : You would want to check to see if that is the case.

ADD REPLYlink modified 22 months ago • written 22 months ago by genomax87k
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