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A detailed analysis permitted the recognition of different possible reasons for such discrepancies: sequencing errors in public sequences, wrong supposed specificity (sometimes due to more recent sequences than the oligonucleotides being evaluated) or even typing errors in the oligonucleotides.
(We could not get access to more recent sequences used in the TRECVID series. The most recent versions are available only for competitors in the TRECVID challenge. All the same, we believe that the 2001 data still provides another independent data set suitable for testing the algorithms).
It would appear that the overall enhancer activity is determined by the combinatorial affect of the ancient and the more recent sequences.
Our sequences from bat isolates and from bat tissue samples also showed perfect matches with sequences deposited earlier by Blehert et al. [14] and with more recent sequences from France, deposited by Puechmaille et al. [18].
Most of these sequences are from isolates collected >30 years ago; only 2 more recent sequences (GPC and L gene fragments) from strain SL06-2057 were isolated in 2006 (17, 19 ).
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More recent sequence comparisons of ycf15 in other plastid genomes also supported the conclusion that this putative gene is not functional [ 9, 39].
A more recent sequencing technology is pyrosequencing, which is based on the principle that nucleotide incorporation in a DNA strand is accompanied by release of pyrophosphate.
The array has broader coverage of bacterial and viral targets and is based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature.
Only with the more recent sequence data from diverse streptophytes such as Cycas taitungensis [ 27], Physcomitrella patens [ 20] and Megaceros aenigmaticus [ 7] does the general pattern emerge that this gene is in fact widely present.
It must also be noted that the prostate cancer case exemplified in this study was performed on the Illumina GAIIx platform and more recent sequencing of WGA MP libraries using the methodology described in this report on the newer Illumina HiSeq platform generated far greater depths of sequencing (Fig. 2f and Supplemental Table S2).
These methods include TA cloning [ 2], ligation independent cloning with T4 DNA polymerase [ 3, 4], GATEWAY recombinational cloning [ 5], and more recent sequence- and ligation-independent cloning kits, such as CloneEZ (GenScript USA Inc., Piscataway, NJ, USA), one step cloning [ 6], and overlap extension PCR cloning [ 7].
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