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This procedure allowed clones with small log2-ratio values to be declared amplified if they were high relative to surrounding clones.
Furthermore, conventional lipofection as a delivery method yielded sufficient numbers of clones with small amounts of starting cells, in contrast to methods based on electroporation [ 1, 7].
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The blue light/darkness fluorescence ratio was calculated for each clone and the clones with smallest ratio were selected for further analysis.
Their approach estimates the size of small clones with little error, but estimates for larger clones have greater error [ 46].
The emu had a larger number of clones with a small number (1 5) of hits, and a smaller number of clones with a large number of hits, than did alligator and turtle (Table 1).
In contrast, BAC clones with very small inserts would provide too little information from HICF for being valuable for physical mapping.
Most small ruminant (sheep and goat) strains belong to a single clonal complex CC133, which includes at least 23 STs, as demonstrated recently by Smyth et al. (2009), consistent with several reports of a widespread S. aureus clone associated with small ruminant mastitis (Jorgensen et al. 2005; Aires-de-Sousa et al. 2007; Smyth et al. 2009).
A few additional clones with inserts smaller than expected (400 500 bp) were sequenced too.
Excessive amounts of either enzyme showed an increase in ligation products containing non-insert clones with a smaller vector fragment.
Considering the clones with no or small inserts were excluded from contig assembly and the average insert size of the BAC clones used for contig assembly should be higher than 132 kb, the BAC clones mapped on contigs (26,466 BAC clones) represented at least 9.4× genome equivalents of the papaya genome.
After excluding the clones with no or small inserts (referred as less than 20 true fragments after editing), and cross-contamination (70% or higher shared fragments for neighboring clones), the remaining 30,824 fingerprints (78.7% of the BAC library) were subjected to contig assembly using the FPC (FingerPrinted Contigs) program.
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