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In the case of sequence errors corresponding to inserted segments (internal insertions, N/C-terminal insertions), 16 of the 23 inserted segments were conserved in closely related organisms, although 5 of them had one or more stop codons.
If DNA sequences have inherent characteristics, which are encapsulated by the polynomial expression, and the inserted segments lead to incompatibility with such characteristics, then such excisions can be understood.
This increase in sequence continuity of manual domains results from imposing evolutionary assumptions on the splits: Compact regions composed of multiple inserted segments could not represent single evolutionary events and were treated in a special category of "composite" domains.
However, the current procedure depends on the somewhat ad hoc assumption that inserted segments exceed a certain length.
Sequencing was performed with a generic T7 primer located 5' upstream of the inserted segments, following the protocol of the PRISM Big Dye Terminator Kit on an ABI3700 or MEGABACE automated sequencer.
Importance sampling was used to make the calculation feasible, where the bond length of inserted segments was chosen from a normal distribution matching the equilibrium distribution of bond lengths, truncated at ± 3 standard deviations.
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The D3 domain of flagellin was replaced with one or more RGD motifs linked by various oligopeptides modulating flexibility and accessibility of the inserted segment.
The sequence of the inserted segment of the recombinant plasmid, designated pCAN46ΔssrA-DD, was verified by DNA sequencing.
Post-recombination, loxP sites are located in cis, flanking the inserted segment.
The second mechanism that can cause a length disparity between an inserted segment and the fragment excised during splicing is when an inserted segment has an internal splice site and its unspliced terminus extends the length of its adjacent exon.
We then sampled six sequence regions of the same size as the inserted segment from the surrounding areas of the plastome.
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