An hmm profile based on an alignment of known RXLR-EER effectors [ 38] revealed one P. ultimum assembly (asmbl_7845) as a putative positive.
Based on an alignment of 85 GRA7 sequences new primer sets that anneal in the highly conserved regions of this gene were designed.
It calculates the subPSEC (substitution position-specific evolutionary conservation) score based on an alignment of evolutionarily related proteins.
We calculated the average Shannon Entropy for each 10-AA segment over the Nef protein based on an alignment of 514 known, independent sequences.
The model was built based on an alignment of profalcipain-2 at 31.2% sequence identity with the crystallographic structure of procathepsin B (25, 26).
Substitutions also were classified by the position-specific relative variability rate calculated from the consensus 23S rRNA model based on an alignment of 187 bacterial 23S rRNA genes [14].
For position 262 genotype 1 and 3 have the R (as the replicon), while most of the genotype 2 and 4 sequences lack this position (based on an alignment with all genotypes).
The software was used to detect the heterozygous position within each electropherogram and to assess the typing, based on an alignment of the processed sequence with a library of HLA sequences and alleles updated to October 2007.
Based on an alignment of the deduced amino acid sequences, we constructed phylogenetic trees.
(B ) Matrix of coupling strengths between pairs of YidC residues based on an alignment of 2366 non-redundant sequences.
Most phylogenetic inference approaches are based on an alignment of homologous sequences (e.g. DNA, RNA, amino acids).
