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Our results suggest that rather than avoiding larger genomes, comparative sequencing projects with aspirations to annotate non-coding DNA would benefit from the inclusion of species with large genomes at an optimal evolutionary distance - far enough for non-functional sequences to have significantly diverged, but not so far as to preclude alignment between the reference and comparison genomes.
Using this strategy, Rmaps harboring major alterations that preclude alignment to the reference were gradually incorporated into the consensus map, extending it into regions that contain more complex rearrangements.
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Both ADH-1 and ADH-2 have nine introns, and between the two genes the corresponding intron sequences are so divergent as to preclude meaningful alignment.
Divergence of the BID sequence precluded unambiguous alignment with the other two proteins and a similar peptide design.
Trees generated from the Pax-C data were rooted using sequences from Isopora cuneata, whereas the mtDNA tree was rooted with A. cervicornis as in this case the degree of divergence of the I. cuneata sequence effectively precluded unambiguous alignment.
For the Asty- and Sly-related trees, we were able to use the X-linked homologue as an outgroup to root the tree, however, for the Ssty-related tree this is not possible owing to much greater divergence of the X homologue which precludes accurate alignment.
A phylogeny derived from amino acid sequences of GroEL proteins is consistent with the phylogeny inferred from rDNA sequences, although the high level of divergence manifest among these genes precludes unambiguous alignment of rickettsial GroEL sequences to homologous sequences from taxa outside the Rickettsiae.
Unfortunately, extensive indel variation and the repetitive nature of these sequences precluded reliable alignments among any of these unigenes.
While this improves speed, it reduces the likelihood of finding the OCS and precludes finding alignments similar to them.
The inclusion of highly variable non-coding regions generally precludes global sequence alignment across land plants, or even angiosperms.
The microsatellites were not included in the analysis because variations in copy number precluded a robust alignment.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com