In addition, the DNA molecule in eukaryotic organisms is larger and nucleosomes are used to compact it introducing pronounced, small scale (sequences consisting of approximately 200 bp), long-range correlation effects not present in bacteria [2].
These findings are consistent with previous small scale sequencing of rice small RNA libraries wherein the expression of miR168a but not miR168b was observed [ 32].
Sanger sequencing has long been the gold standard sequencing technology and remains an important method for small scale sequencing experiments and routine genetic diagnostics.
Small scale sequencing of 384 random clones confirmed the directional aspect of the inserts, the plant nature of the source cDNAs, and the frequency of positive clones.
By contrast, the low number of ambiguities in coding regions [ 23] in such a small scale sequencing project would allow the use of a Sanger sequencing approach as an alternative cost-efficient way to correct ambiguity in those regions, and insure correct annotation of genes.
In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors.
Thus changes of intron-exon structures by small-scale sequence changes may be rare events in evolution.
Rather, we surmise that the same mechanism is responsible for both large-scale sequence read depletion from chromosomal arms and small-scale sequence read depletion from exons with high G/C content.
To initiate a small-scale sequence survey of the prairie vole genome we attempted to generate BAC-end sequences (BESs) from all clones corresponding to library plates #1-4, as well as those clones identified in the above targeted mapping efforts.
In the context of base pair substitutions and other small-scale sequence mutations, searches for conservation have utilized baseline mutation rates estimated from rates of changes for various classes of putatively neutral sites (e.g., synonymous or intronic sites) in order to identify slow-evolving and thus putatively functional sequences.
Changes can occur either by gain or loss of a large amount of genomic sequence (for instance by complete or nearly complete loss of one or more complete intron or exon; [ 3- 8]), or by the evolution of new splicing patterns for existing sequence due to small-scale sequence changes ([ 9, 10]; more complex cases are also possible).
