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Most indels identified in this sequencing effort were flanked by identical sequence.
Some polymorphisms in the proximal promoter of membrane transporter genes identified in this sequencing effort have been shown to alter transcription rates in reporter assays and associate with expression levels in human lymphoblastoid cell lines [13], [14].
The SOLiD platform exhibited the lowest base substitution error rate, likely reflecting the di-base encoding and color space scheme in this sequencing technology.
In this sequencing effort we have identified a transcript contig that is a BLASTX match to an A. capsulatus α-box protein (GenBank accession ABO87596), but does not align to the genome assembly.
Further improvements in this sequencing technology, and in the related computational methods, will enable more information to be obtained at a lower cost [ 42] (see also a recent application in [ 43] and the evolution of computational approaches from [ 44- 46] to [ 47]).
The presence of the exogenous DNA in this sequencing run was evident from the near sequence identity of a number of contigs with the high-GC fraction of C. remanei and also from the analysis of k-mer coverage distribution (Fig. 3).
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