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See Fig. 4 for an example alignment of different LAT protein sequences highlighting the important motif residues.
As an example, alignment of the gA and gB SPA orthologous regions of respectively 31 498 bp and 18 589 bp correspond to a cumulative CNS length of 11 152 bp with 85.9% of sequence identity and 0.874, 0.664, 1.3 values for respectively Ks, Ka and Ks/Ka.
An example alignment of a conserved microsatellite is shown together with the phylogeny used in our analysis (fig. 1).
An example alignment of 112 Gbp of Illumina GA data requires 116 GB of disk space (1.0 byte per input base), including sequences, base qualities and all the meta information generated by MAQ.
An example alignment of P. berghei (PBANKA_030400) and yeast AROM complex is provided in Figure 5, while the remaining alignments have been provided in Additional Files 12, 13, 14 and 15: Supplementary Figures 9, 10, 11 and 12.
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As an example, alignments of barley CLS-F6 (GenBank:EU267181) and the oat homologue (GenBank:GQ379900) with dnOST revealed homology to five isoforms (Additional file 14).
Figure 10 c is an example multiple alignment from which the profile HMM given in Fig. 10 b could be learnt.
Figure 9 is an example Dotter alignment of two Huge Repeat contigs, [GenBank: NT_161892] and [GenBank: NT_161926], demonstrating that high sequence homology extends across the entire contig, genic and intergenic regions included.
As an example, the alignment represented in Figure 4 shows that specimen 90 comprises two different recombined ITS sequences resulting from the same PCR reaction, that could be the result of jumping PCR.
Figure 4a demonstrates an example of alignment reported by DOMAIN between 10 yeast proteins and three worm proteins, in which nine of the yeast proteins (all except Nyv1) and all three worm proteins are known to be involved in the pathway of SNARE interactions in vesicular transport in KEGG (Kanehisa and Goto, 2000).
One example alignment and predicted precursor position is shown in Figure 2A.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com