To test larger problems, we used PAGAN and the best alternative method, hmmalign (Eddy, 2011), for a re-analysis of metagenomic data of Mirarab et al. (2012) consisting of reference alignments of 500 sequences and addition of 5000 sequence fragments.
The best alternative method was the oligo analysis tools, which return patterns that reasonably match the consensus patterns of all six inserted motifs, however, only consensus sequences are returned, with no distinct positioning information.
Despite some concerns (low sensitivity and specificity for some diseases) regarding this approach, there is general agreement that VAs are the best alternative method available for low-income countries to understand cause of death patterns in the absence of national vital registration systems.
Until recently, the best alternative method available was intracellular labeling of proteins fused to polypeptide tags (e.g. SNAP, HALO, or TMP tags) but this still implies large protein fusions (e.g., SNAP tag: 20 kDa; Jones et al. 2011; Hinner and Johnsson 2010; Keppler et al. 2003; Wombacher et al. 2010).
Specifically, ClausIE produced 2.5 to 3.5 times more correct extractions than OLLIE, the best-performing alternative method.
Molecular methods based on the amplification of nucleic acids for microbiological analysis of water quality show enormous potential and are considered as the best alternative to culture-based methods.
While therapies can be easily selected based on a criterion of nominal performance, the importance of SSV application is apparent in presence of parametric uncertainty, when, to the best of our knowledge, alternative methods are not available.
The model developed considers parameters influencing the carbonation process and enables the user to choose the best alternative of the machine based methods.
The use of customized QT correction methods, such as the individual QT correction (QTcI), based on individual regression models computed from a set of QT/RR measurements collected during drug free periods, has been promoted as the best alternative to the universal correction methods [ 23].
Ministers said that the EYFS would help improve the standard of childcare, and dismissed critics who say it will be misused in substandard settings and will shackle the best settings and those which use alternative methods.
