Protein sequences were aligned using MegAlign (DNASTAR) for multiple alignments and EMBOSS http://www.ebi.ac.uk/Tools/emboss/align/index.html for pairwise alignments.
The multiple alignments and trees were used as input for MAPP43.
NCBI Blastn, multiple alignments and conserved domain search showed that BnECR had the highest homology to A. thaliana AtECR.
Multiple alignments and phylogenetic relationship strongly suggested that VpCLYZ-1 and VpCLYZ-2 belonged to the c-type lysozyme family.
Multiple alignments and phylogenetic analysis strongly suggested that RpPLYZ was a new member of the phage-type lysozyme family.
We then describe an extension of the pairwise alignment method to MSA using a novel approach that is based on a poset representation of multiple alignments, and an efficient online topological ordering algorithm.
Michael Hiller and Saatvik Agarwal generated the pairwise and multiple alignments and the CNE set, Jim Notwell applied transitivity, Michael Hiller applied ancestral reconstruction and Aaron Wenger contributed tools and to the data analysis.
We found that the AL-A gene was highly homologous (90%) to the sequences from the pea plastocyanin via multiple alignments, and the deduced protein precursor was predicted to be chloroplast-specific via the ChloroP computer program.
Multiple alignments and minor adjustments of the sequences of these isolates were performed using clustal X 1.81 (Thompson et al. 1977) followed by BioEditor software.
At the same time, the protein network can illustrate biological information in a more powerful and effective view, which could not be easily achieved by multiple alignments and large trees [5].
After removal of poor quality, multiple alignments, and duplicated reads, 30 40% of reads remained.
