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For signal combination, the spectra of the residual background noise after noise reduction are aligned among the Q output signals.

Approximately 150 bp of sequence upstream from the start codon could be aligned among the three Latrodectus genes and ∼300 bp upstream sequence between L. hesperus MaSp1 and MaSp2.

In the PowerMatch module, the metabolite features are aligned among the samples taking into account the similarity of MS/MS fragmentation patterns.

Fifteen species within the Fusarium fujikuroi species complex clade were selected for phylogenetic analyses and sequences of the BT2 and TEF-1α genes were aligned among the sequences available from GenBank (Additional file 1: Table S1).

In a set of 5,015 orthologous genes unambiguously aligned among the four species, we show that, except for tri- and hexa-SSRs, for which insertions and deletions are frequently observed, SSRs in coding regions evolve mainly by substitutions.

Nucleotide sequences for each of the 37 genes were aligned among the newly sequenced 10 taxa and 39 other vertebrates (see Table 1 and Additional File 3 for their taxon names and accession numbers).

At the fourth step of the workflow in Figure 3A, the retention time (RT) grids on each MS chromatogram plane were perfectly aligned among these 92 samples (Fig. 3B), which allowed the solid quantification analysis of multiple samples.

There are only two regions that could be unequivocally aligned among all the ciliates and of which the alignment did not depend on the program used [ 20, 21].

We also found that the dicot IR sequences near the IR-LSC junctions varied little and could be aligned among orders having the same or different IR-LSC junction types, while in monocots the corresponding regions were very different and difficult to align across different orders (Fig. 2B).

Sequence alignment showed extensive amino acid variability in the C-terminal region of the merlin proteins of various species, while a noncontiguous stretch of 25 amino acid residues, including the well-defined actin-binding site, was reliably aligned among all predicted ERM proteins with the exception of the "unnamed protein 2" of Tetraodon nigroviridis.

To identify SNPs, full-length genomic DNA of all 11 candidate genes were sequenced and aligned among 40 unrelated individuals from the association population of P. tomentosa, without considering insertions/deletions (INDELs).