Sequence pairs from human and mouse were aligned using EMBL-EBI Align using the Needleman-Wunsch global alignment algorithm [ 39] and the BLOSUM62 transition matrix [ 40].
In the last round of the multiple alignment, either the POG of human, dog and mouse is aligned to the rat genome or the POG of mouse, rat and human is aligned to the dog genome.
As a first step in understanding the evolutionary relationships among the members of the BPI-like family, the sequences from the intact genes within the BPI-like locus in cattle, human and mouse were aligned and a phylogenetic tree was constructed (Fig. 4).
p: promoter; h: human; t: tammar; F: forward primer; R: reverse primer; D: deletion Sequences from the tammar, opossum (representing another marsupial species; Monodelphis domestica), human and mouse were aligned using MULAN to investigate the conservation of the WNT4 promoter region.
The base of the mouse tail was aligned with and taped to the bottom of a centrally located, vertical, flat, metal bar that was connected to a force transducer which recorded the time the mouse spent in an immobile state.
Lambda was located through the skin, still transparent at P1, and the mouse head was aligned in a model 900 stereotactic instrument (Kopf Instruments, Tujunga, CA) for the lambda, and the point 3.7 mm anterior from lambda, being in one horizontal plane and lying on the longitudinal axis of the instrument.
The resulting sequence was aligned to mouse genome build GRCm38 to identify the transposon-flanking genomic sequence (i.e., insertion site) and determine which gene was disrupted based on current annotation for build GRCm38.
Sequenced DNA was aligned to the mouse genome (mm9) using Eland or Bowtie [ 27].
The mouse Nav1.2 used in this study was aligned with the human family members.
Briefly, raw 50 bp reads was aligned to the mouse genome (MGI, as of Feb 15 , 2012 using Bowtie (Langmead et al., 2009).
