The total sight distance deficiency of an alternative alignment is estimated based on (i) the length of the road segments where ASD < SSD and (ii) the significance of sight distance restriction.
In 1957, Dade County Commissioner Ralph Fossey proposed an alternative alignment of the Palmetto Expressway.
The reproducibility of the alignment approach was tested by performing the mapping step with BWA, an alternative alignment program [ 45].
Manual clone-by-clone alignment and gene annotation as well as repeat and SNP/haplotype analyses result in an alternative alignment significantly improving the DEF locus representation.
Lastly, we repeated benchmark 2 with an alternative alignment template implementation relying on column profiles rather than a PO-MSA for comparison.
In each case, the reads involved were realigned with the CB4856 genome using cross_match (P. Green, unpublished data), providing an alternative alignment method and a full Smith Waterman alignment of the read against the genome, and analyzed.
To test the accuracy of the tree topologies generated by the ClustalW alignments and Bayesian analysis, each group was also subjected to an alternative alignment by Muscle [ 60] and mafft [ 61] and alternative phylogenetic analysis by maximum likelihood (ML) using phyML [ 62] with LG and JTT substitution models and rate heterogeneity.
The result is an alternative alignment shown in Fig. 1B, which differs from the hg16 assembly in three major points and is supported by a detailed repeat and SNP/ haplotype analysis: (1) Clones 23 27 not present in the hg16 assembly were located distally of the gap, whereas clones 11, 12 and 17 were excluded since they cannot be aligned according to our criteria.
When all alternative alignments have been evaluated, a statistical assessment is performed to compare the distribution of their predictor scores.
First, it should be possible to obtain reliable models for each alternative alignment.
For each alternative alignment, the MODELLER program [11] is used to build an ensemble of one hundred models, all solutions of the same distance geometry problem, but with different initial conditions for the molecular dynamics optimization step.
