Question: Fosmid contamination in C. elegans genome?
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gravatar for gtrwst9
11 months ago by
gtrwst90
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 • 377 views
ADD COMMENTlink modified 11 months ago by Ahill1.6k • written 11 months ago by gtrwst90
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gravatar for Ahill
11 months ago by
Ahill1.6k
United States
Ahill1.6k 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 11 months ago by Ahill1.6k
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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 11 months ago • written 11 months ago by genomax71k
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