4) Duplicate insert marking.
On the one hand, single-nucleotide polymorphisms alter the base at a single position of the nucleic acid polymer; on the other hand, huge mutations called chromosomal rearrangements can move around, duplicate, insert, or delete huge blocks of DNA, often from one chromosome to another.
Duplicate inserts were used for each separate cell line analyzed.
To demonstrate the sensitivity of the 3-D cultures, BAC at concentrations of 0.005%, 0.01%, 0.025%, 0.05%, 0.075% and 0.1% and saponin at concentrations of 0.01%, 0.05%, 0.1%, 0.25% and 0.5% were incubated in duplicate inserts for 60 minutes at 37°C.
For a single Ds1 insertion event, providing one donor and one acceptor indicates incorporating the inserted introns messages, both upstream and downstream the Ds1 plus an additional duplicate insertion site sequences (8 nucleotides).
The second strategy is where snoRNAs may duplicate and insert into a new host gene or a paralogous host gene in a different genomic location, and is termed trans-duplication [ 12, 13].
Intrachromosomal duplications in which the duplicate is inserted in the reverse direction (inverted duplication) are likely to be a major source of false positives for this analysis.
However, tandem duplications of one gene are indirectly taken into account: they cost zero (as the gain of an adjacency between two children of a duplication node is costless; see Section 2), while a non-tandem duplication of one gene can cost one breakage plus two gains when one duplicate is inserted between two other genes.
We observed three distinct patterns of duplication events for B3 genes according to their duplication origin: genes that were duplicated and inserted in different chromosomes, genes that were duplicated and inserted in the same chromosome and genes that were duplicated in tandem.
As there was a duplication of the lipoprotein gene in B. burgdorferi 29805, it is possible that the BBU29805_G01 was duplicated and inserted at the BBU29805_I30 genomic site, but that only BBU29805_G01 and its associated stem loop sequence was transferred.
Type II: duplicated gene inserted at a locus where no prior gene existed.
