For instance, PTMap [ 43] utilizes sequence alignment to localize sites of PTMs on target proteins while substantially reducing false-positive identifications based on unmatched peaks.
Sequence alignment for T3SS and non-T3SS secretin domains.
Mirarab, S. et al. PASTA: Ultra-large multiple sequence alignment for nucleotide and amino-acid sequences.
Multiple sequence alignment for each gene segment was performed using MAFFT v7.05835.
A large proportion of these algorithms utilize sequence conservation within a multiple sequence alignment (MSA) of homologous sequences to identify intolerant substitutions, for example, a substitution falling within a conserved region of the alignment is less likely to be tolerated than a substitution falling within a diverse region of the alignment (see reference [ 40] for a review).
RC-seq utilizes sequence capture to enrich DNA for the junctions between retrotransposon termini and adjacent genomic regions, followed by paired-end sequencing, alignment, and clustering, to reveal L1 insertions absent from the reference genome.
Putative amino acid sequences were used to guide nucleotide sequence alignments for the protein-coding genes.
Sequence logo representation (below) of multiple sequence alignments for C. tritonis with other species (Supplementary Data S8).
Extended Data Fig. 4 Sequence alignments for different functionally important regions of mtIF2.
The Pfam database, utilizing multiple sequence alignments and hidden Markov models (HMMs), uses sequence similarity to formulate protein family classifications [16] and serves as a useful tool for exploiting these relationships.
The high ranked linear and conformational B-cell epitopes derived from several online web-servers (e.g., ElliPro, BepiPred v1.0, BcePred, ABCpred, SVMTrip, IEDB algorithms, SEPPA v2.0 and Discotope v2.0) were utilized for multiple sequence alignment and then for engineering the vaccine construct.
