A HMM profile was constructed based on the alignment of protein sequences corresponding to the seven known bovine cathelicidins.
For each group of orthologs, we obtained aligned nucleotide sequences based on the alignment of the peptide sequences, which we generated with MUSCLE [76].
Based on the alignment result, the RAD-based SNP calling was done by SOAPsnp.
Sequence alignment was done using transAlign, which aligns protein-coding DNA sequence based on the alignment of amino acids [ 51].
For reasons of comparability with MIF descriptors, sequence descriptors based on the alignment were calculated.
Slopes are then further partitioned based on the alignment between slope angle and dip angle.
A Neighbor-Joining phylogeny analyses was performed using MEGA5, based on the alignment results in Additional file 1: Figure S4.
Fig. 1 Phylogenetic affiliation of the isolate LAMAI 31 based on the alignment of 18 β-tubulin gene sequences.
The algorithm is mainly based on the Alignment Score Matrix (ASM) computation by comparing input motif with full length sequence.
First, slopes are classified into three functional types based on the alignment between the dip azimuth and slope aspect.
