In many cases the location of NEP- and PEP-promoters were not experimentally known and were identified de novo in our analyses of multiple alignments of relevant leader regions as described in [ 3].
Following alignment of the relevant DNA sequences, two primer sets were designed to specifically target the Theileria spp. 18S rRNA and Anaplasma spp. 16S rRNA gene sequences.
Figure 4 Alignment of the relevant region of the sequenced EPG1 promoter, driving the expression of FLO5 in the recombinant yeast, with the original EPG1 promoter found in the wild type K. marxianus strain.
A phylogenic tree was constructed based on the alignment of the relevant matches by using the component AlignX of the bioinformatic software suite "Vector NTI Advance" (InforMax, United States).
The Insertion type was classified as exon or intron based on an alignment of the relevant FST, MAGI and ZMGI sequences.
An alignment of the relevant part of the polypeptide sequence, comprising the presumed signature residues at positions 108, 120, 138, 163 and 199, is shown in the Figure, panel B, for all FIPV and FECV genomes sequenced in this study.
High-resolution methods such as comparative molecular field analysis (CoMFA) (41, 42) and comparative molecular similarity indices analysis (COMSIA) (43) require the alignment of biologically relevant 3D conformations of molecules with a common substructure to generate a map of regions important for the structure−activity profile of a given related series of molecules.
Numbers of synonymous substitutions (Ks) per site were computed with the program yn00 at the online tool Phylemon 2 (http://phylemon.bioinfo.cipf.es; [ 28]) in which PAML version 4.4c [ 29] is implemented, using nucleotide sequence alignment of the relevant gene pair for protein-coding regions.
Multiple sequence alignments of the relevant protein regions were generated by CLUSTALW http://www.ebi.ac.uk/Tools/clustalw2/index.html and the alignment uploaded for JPRED analysis in the "advanced" mode.
However, PROmer alignments of the relevant B. mori and H. melpomene scaffolds revealed no other homology [i.e., synteny] between these genomic locations.
