Angular changes between RF3-conformations were estimated based on alignment of amino acid residues 97 105, 121 133 and 328 343.
To understand the relation between sequence similarity functions, a number of tools based on alignment have been integrated.
Discordances between BtOM1.0 and the UMD3.1 were called based on the alignments between the consensus maps that were trimmed and stripped off from the last (8th) cycle of iterative assembly (Fig. 1; Methods; [ 26]) and then manually curated.
Based on the alignments between tRNAs and sequenced small RNAs, we identify a unique characteristic suggesting independent pathways of tRNA processing.
To identify larger insertion/deletion events, we developed a customized algorithm called BreakPointRead that detects indels based on BLAST alignments between read sequences and the reference genome.
In a first step, estimates were only based on pairwise alignments between human and all other species (fig. 1 A and B ) instead of branch-specific estimates based on multiple alignments (fig. 1 C ).
Relatively high confidence predictions of new possible mutation points are assigned to the mutations predicted based on calculated alignments between genomes from different dengue serotypes (DENV-1, -2, -3, and -4).
Candidate genes (Table 2) for the gene expression analysis using quantitative real time PCR (qRT-PCR) were selected based on unambiguous alignments between NWS unigenes and D. melanogaster annotated genes.
To investigate the selection pressures imposed on the novel exons identified by comparative analysis of cross-species EST libraries, we calculated the evolutionary rates (dn, ds, and dn/ds) based on the alignments between the identified ASVs (including the novel exons and their flanking exons) in the target species and their corresponding EST sequences in the subject species (Methods).
