The 15 amino acid substitutions present in this alignment (substitutions shown in supplementary material S10, Supplementary Material online) generally had a low cost of replacement based on several substitution-cost matrices (Adachi and Hasegawa 1996; Gilis et al. 2001).
In addition, structural comparison based on distance matrix alignment (DALI), class architecture topology and homologous superfamily (CATH) and combinatorial extension (CE) methods revealed that porcine MSP has a novel structure with a new fold providing valuable information for future structural studies on other MSPs and for understanding their biological functions.
a Sequence similarity matrices are based on ClustalW alignments (IUB matrix for DNA or Gonnet matrix for protein sequences) and distance calculations using the Tamura-Nei method on DNA or the Poisson correction on the amino acid level, respectively, with the pairwise deletion option; calculated with MEGA4 (see Methods).
The algorithm is mainly based on the Alignment Score Matrix (ASM) computation by comparing input motif with full length sequence.
The experiment was run by choosing different initial sets of fragments to make and apply a rotation matrix based on the alignment procedure.
We have scored each splice site using a position-specific weight matrix (PWM) based on the alignment of all 5' and 3' splice sites in the C. elegans genome (Methods).
Based on this alignment, a distance matrix is calculated using the Kimura algorithm, which is used as input for the neighbor joining method (both algorithms realized in the PHYLIP package).
The nucleotide alignment was generated based on the protein alignment using codon alignment.
To identify which genomes could be aligned together, we built a composite likelihood distance matrix based on the concatenated alignment of protein-coding genes cox1, cox2, cox3, atp6, atp8, and atp9.
The potential effect of the different missense mutations was then evaluated by using the SIFT software (Sorting Intolerant From Tolerant; http://sift.jcvi.org/) that uses PSI-BLAST alignments, and the PARSESNP software (Project Aligned Related Sequences and Evaluate SNPs; http://www.proweb.org/parsesnp/) to provide a position-specific scoring matrix based on alignment blocks.
