Our criterion to choose among several such paths is to minimize the edit distance between the path and the region sequence.
As it does not vary between experiments, the scaffold (constant region) sequence is encoded within the expression plasmid [ 23].
A comparison of the overlapping region between the BAC sequenced by the Sanger method and the corresponding region sequenced by GS FLX pyrosequencing (i.e., the region between the BAC-ends S0070O23-T7 and S0022P24-SP6 in Fig. 6), identified two gaps of 893 and 151 bp in the GS FLX assembly.
We saw no obvious correlation between the position of the region of sequence similarity and the folding structure hypothesized by either program.
To identify the genomic location of the vanA transposon and its relatedness within and between participants, we analysed the region of sequence adjacent to the transposon in each isolate.
These genes, encoded on opposite strands, share a 1536-nt intergenic sequence; however, the span between the region delimited by their 5′ leader sequence is only 120 nt and presumably harbors their respective promoters.
There is a significant overlap between the regions of the sequence found to be solvent-exposed from the present study and those previously identified to be critical in the rate-determining steps of aggregation from protein engineering approaches.
Although there is significant sequence identity shared between the regions, the lengths of the sequences fail to show the entire shared orthology.
We computed a distance matrix from all the mutations detected in the primary regions and in the three recurrence regions, establishing a phylogenetic relationship between the sequenced regions.
We used web based Genomicus synteny browser [ 68] and Ensembl genome browsers [ 34] to assess the synteny between regions sequenced for X. helleri in this study and five other teleost genomes for which data were available (Ensembl assembly versions: medaka-HdrR; stickleback-BROAD S1; Tetraodon-TETRAODON 8.0; fugu-FUGU 4.0; zebrafish-Zv8).
