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When the number of the annotated genes with reliable significant signatures was compared, the SBS library had about 57.4% more genes (13,964) than the MPSS library (8,871; Fig. 4b, Table 1), suggesting a much deeper coverage in the SBS library for transcriptome survey.
For yeast recombination studies or for analyses of more complex genomes, however, much deeper coverage is required.
This may indicate that 454 EST sequencing has much deeper coverage of L1 stage mRNA sample or, alternatively, the potential novel splice variant shows a relatively higher level of expression at the L1 stage.
This conclusion is supported by the fact that the much deeper coverage with ESTs (> 150,000; [ 27]) of the D. discoideum genome was not sufficient to cover most of the genes.
The greater efficiency of discovery, including variants that are expressed at low levels, derives from the much deeper coverage of the sRNA population provided by pyrosequencing, and avoidance of cloning in the 454 system.
Due to the much deeper coverage of the transcriptome by this technique, almost all differentially expressed transcripts represented in the SSH libraries have at least one, but usually more counterparts in our 26 bp tags libraries.
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Newer technologies typically produce shorter reads at greatly reduced cost and allow the completion of projects with much deeper sequence coverage using many more reads than a Sanger-based project.
454 FLX Titanium is a massive pyrosequencing strategy which generates medium-size single reads uncovering large amounts of DNA sequences providing much deeper sequencing coverage than it is possible with conventional Sanger sequencing [ 40].
The problem of incomplete representation of protein-coding transcripts will likely be solved in the near future, when reduction of sequencing costs and an increase in sequencing throughput will allow a much deeper sequence coverage even for non-model species transcriptomes.
In fact, despite having a much deeper sequencing coverage, the draft genome assembly using male reads alone has a smaller N50 length (the scaffold size above which 50% of the total length of the sequence assembly can be found, Table 1) than that derived from female reads (9.9 kb vs. 12.6 kb).
It goes much deeper than partisan differences over birth control coverage and abortion.
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