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.
The reproducibility of the alignment approach was tested by performing the mapping step with BWA, an alternative alignment program [ 45].
Furthermore, an optimality criterion has to be specified that determines which of two alternative alignments of a putative TR locus with its perfect counterparts is to be preferred.
These methods will be integrated into a highway alignment optimization model (HAO) previously developed by the authors to evaluate numerous possible alternative alignments of a new highway system through tradeoffs among various relevant decision criteria.
In order to estimate the existence of such a non-parametric correlation, we computed alternative alignments of each available dataset using seven methods: ClustalW (Thompson et al., 1994), Mafft (Katoh et al., 2005), Muscle (Edgar, 2004), PCMA (Pei et al., 2003), POA (Grasso and Lee, 2004), Probcons (Do et al., 2005) and T-Coffee (Notredame et al., 2000).
Result: We developed STRIKE, a method that determines the relative accuracy of two alternative alignments of the same sequences using a single structure.
Several alternative alignments of the analogs gave r2 values in the range of 0.8 0.95.
We use sets of analyses, employing different methods typically used in barcoding, on two alternative alignments of the inversion region.
In contrast, the alternative alignments of the key helices 3 and 6 were "worse" with respect to the overlap of Na-ligands (cf. Additional file 1: Figures S2B and S3B).
Our goal was not so much to estimate the MSA accuracy in absolute terms, but rather to tell apart two or more alternative alignments of the same structure/sequence pair.
