To validate these variations, the following approaches were performed based on alignments of all available Illumina reads for TM-1 and Hai7124 to the TM-1 (v2.1) and Hai7124 v1.11) genomes by BWA (version 0.7.15-r1140 62.
Consensus primers, degenerate primers and virus-specific primers, whose designs were based on alignments of available cherry flexivirus sequences, were tested to amplify viral genomic fragments of six CGRMV isolates and one CNRMV isolate.
All 5' targeting sites were chosen based on alignments of partially sequenced field samples (Accession numbers EU787517.1 – EU787984.1, AY462581.1 – and62851.1) and the published 3d7 var gene sequences.
Consistently, the models with the strongest scores were based on alignments of PL domains of ZIP proteins with PrP or Dpl structures and all attempts to align the ZIP PL domain to structural templates outside the prion protein family produced insignificant fits.
To assess the extent to which relatedness of cluster sequences across strains reflects shared host-or tissue-specificity, a phylogenetic tree for each cluster was built based on alignments of concatenated sequences of the predicted gene products of that cluster (Figure 2).
Described alternatively spliced isoforms are based on alignments of ESTs and cDNAs onto these gene models.
Intron boundaries were determined based on alignments of the exon amino acid and nucleotide sequences.
Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences.
This benchmark tree was constructed based on alignments of 70 universal single-copy genes.
Initially, we attempted an SNP discovery approach based on alignments of ESTs.
For phylogenetic inferences based on alignments of orthologous sequences the super-matrix and super-tree approaches were used.
