Fosmid contamination in C. elegans genome?
1
0
Entering edit mode
3.3 years ago
gtrwst9 • 0

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 • 739 views
ADD COMMENT
0
Entering edit mode
3.3 years ago
Ahill ★ 1.9k

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 COMMENT
1
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2449 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6