The paralog picker was not perfect; there were still alignments with apparent paralogous gene copies after its application.
Still, the alignment of 1199 with Mr. Pataki provides the governor not only with the benefit of Mr. Rivera's get-out-the-vote operation, but a potentially large union budget to pay for advertisements and mailings.
Kalign2 (Lassmann et al., 2009) is one of the fastest MSA methods, and still the alignment accuracy is comparable to many of the slower methods.
The paradox is that, for the latter type of pinning site, one still observes alignment of Ld domains along the actin fibers, albeit weak.
The analysis of splicing by RNA-Seq has many caveats of statistical power, and there are still serious alignment errors that make accurate assessment of splice junctions problematic (Sturgill et al. 2013).
However, optimal alignment still remains a matter of controversy, as several recent reports have found little or no correlation between postoperative tibiofemoral malalignment in the coronal plane and revision rates (Morgan et al. 2008, Parratte et al. 2010, Bonner et al. 2011).
For the remaining datasets of BAliBASE, all consistency-based programs, namely Probcons, T-Coffee, Probalign and MAFFT still produced alignments with higher accuracy when compared to the other five programs.
Our library subtraction protocol enabled us to reduce the redundancy typical of EST projects so as to maximize the number of new genes identified and still have alignments deep enough for polymorphism identification.
Nevertheless, targeted alignment can still be used as a sensitive method for finding preselected gene fusion events.
Thus, we sought pairs of RNAse P RNAs that are highly conserved, and yet their alignment can still benefit substantially from unordered mappings.
