Amino acid sequences from segmentally or tandemly duplicated pairs were first aligned and then guided and transferred into a cDNA sequences alignment using in-house Perl scripts.
Additionally, the initial and terminal regions of the multiple sequences alignment had, in some cases, to be removed because they were poorly aligned.
b Protein sequences alignment of OsSND2 and AtSND2.
Fig. 6 Multiple sequences alignment of REL2 with its highly similar protein sequences and phylogenic tree.
A Amino acid sequences alignment of native IFN-CSP and Mu-IFN-CSP.
After that, a multiple sequences alignment was carried out and evolutionary tree was constructed.
Multiple sequences alignment showed the deduced amino acid sequence of Pr-SR is similar to scavenger receptors of other lepidopterans.
Residues G71, I74 and F91 that located in the substrate-binding pocket were selected to be substituted according to sequences alignment and homologous modeling.
Furthermore, based on the results of protein sequences alignment, we constructed a neighbor-joining phylogenetic tree of these 27 proteins (Fig. 7).
The putative protein architecture (domains and other important motifs) was determined and, amino acid sequences alignment and phylogenetic analysis of both receptors together with IGF-IR orthologues from different vertebrates was performed.
Sung et al. [4] proposed an anomaly based detection using API call sequences to detect unknown and polymorphic malware using an Euclidian distance measurement between API sequences alignment of different call sequences.
