We performed two separate analyses of our conserved clusters, one based on alignment of nucleotide sequences and another based on alignment of predicted peptide sequences.
1) Unable to annotate many reads - Methods that rely on alignment of reads/contigs to known genomes still fail to align a large number of reads if they are from unknown species.
Phylogenetic analysis from MEP/carotenoid enzymes pathways was based on alignment of concatenated sequences from 29 plant species and one moss species.
Phylogenetic reconstruction from proteins codified by a set of 13 single copy genes identified by Duarte and co-workers [ 21] was based on alignment of concatenated protein sequences from 28 plant species and one moss species.
Based on alignment of available and newly generated partial 5′-UTR nucleotide sequences, one forward and two reverse primers were designed, which amplify a 104 bp PCR product.
"Clients are placing a growing emphasis on alignment of interest," said Daniel Pinto, managing director of Stanhope Capital, a family office that, like Sand Aire, is based in London.
Ideal positioning for each implant was determined based on alignment of the implant neck and head within the original bone (Fig. 1).
In this study, we selected 10 divergent epitope candidates based on alignment of the EV71 and CVA16 P1 amino acid sequences using the Multalin interface page, and these epitopes are conserved among all subgenotypes of EV71.
In this study, based on alignment of 70 full-length HEV sequences of genotypes 1 4, a part of the ORF2/ORF3 overlapping region was found to be the best target region for PCR amplification of various HEV strains.
Whereas the cladogram in Fig. 1 is based on alignment of proteins, we used gene names for clarity.
