The latter alignment option was used in this study for the binding mode analysis of FXR ligands.
The latter alignment case provides solidification conditions where the impact of gravity during solidification is strongly reduced.
The latter alignments are longer and more accurate, but selection of the subset of residues requires knowledge of the native structure; this is not the case for (2).
Building on this latter hypothesis, sequence alignment between the BAC construct used in our study and the one used by GENSAT suggested that the additional regulatory regions may be present in human-DNA homologous to the large non-overlapping 3′ mouse-BAC region.
This adjustment permitted more optimal global alignment of the putative parent in instances when the latter aligned only partially and to the extremity of the candidate region in the BLAST step.
During this latter step, we ultimately removed three alignments that were confounded by gaps, resulting in three genes with preliminary evidence of selection before correction for multiple testing.
This latter figure provides the percentage of columns in the alignment where the alignment depth >= 2. MSAs with a % identity > 95% were considered further.
This latter was checked and edited by hand to remove alignment uncertainties.
This latter was checked and edited by TrimAl to remove alignment uncertainties (http://phylemon.bioinfo.cipf.es/utilities.html, last accessed October 31, 2014) (Capella-Gutierrez et al. 2009).
Using this latter probability, which applies when heterozygosity does not affect the alignment of the BAC fingerprints, the expected percentage of two-haplotype contigs was calculated separately for each class (n = 2 to n = 7) of multi-anchor contigs.
