An alignment of the various eIF3d sequences reveals the existence of several sets of conserved amino acids distributed throughout their length which are good candidates for studies investigating eIF3d function (Additional file 1: Figure S4).
DWM also generated a concatenated alignment of various cyanobacteria.
A sequence alignment of various nsLTPs was made using the ClustalW implemented in MEGA 5 software, and the alignment was manually inspected and adjusted via Jalview (http://www.jalview.org/).org/
This is achieved by mapping of a conservation score derived from a multiple sequence alignment of various SH2 domains ('sh2.aln') onto a representative structure (PDB: 3IMJ) (DeLorbe et al., 2009) and identifying residues in direct contact with the ligand.
Our Additional file 1 displayed a multiple sequence alignment of various eEF1A1 (10 species) and eEF1A2 (9 species) orthologues from vertebrates.
A multiple sequence alignment of various other putative caspases in plants and protozoans was performed with ClustalW (Thompson et al. 1994) and a highly conserved domain was identified that spanned ~144 amino acids.
The first fragment successfully amplified from D. folliculorum was a fragment of the 12S rRNA gene, which was obtained using degenerate PCR based on an alignment of 12S rRNA from various arthropods.
We prepared mRNA from the spleen of individuals of each species and performed RT-PCR experiments using two oligonucleotides designed on the alignment of various elasmobranch Igμ heavy chain sequences available in GenBank.
Primers and probes for the rRT-PCR were designed from the conserved region of the M1 genome segment 5′ end based on the whole-genome alignment of various ARV strains, including six field variants or novel strains obtained in PA poultry.
Fig. 2 Alignment of various DyP-type peroxidase sequences from P. sapidus (PsaDyP), P. ostreatus (PosDyP, NCBI: CAK55151), B. adusta (BadDyP, NCBI: BAA77283), A. auricula-judae (AauDyP, NCBI: AFJ79723) and M. scorodonius (MsP1, NCBI: BOBK71).
