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Again, discrepancies between actual protein lengths and length of the alignment reflect the presence of indels.
More specifically, the clusters observed using a single gene maximum likelihood comparison or Gepard dotplot alignment reflect the same clustering that is observed when whole genome comparison is used.
For example, does the current taxonomic alignment reflect distinct taxonomic groups as defined under the genealogical species concept (i.e., all individuals assumed to represent the same taxonomic group form a monophyletic lineage to the exclusion of any putative heterospecific samples [ Baum and Shaw 1995])?
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A current astral alignment reflects "your immense sensitivity and deep, secret propensity to be powerful," purrs last weekend's posthumous bulletin for Scorpios.
For polymers, tagged with fluorescent dyes, such alignment reflects in the components of polarization of the fluorescence.
But analysts say that while the new alignment reflects a renewed determination from key power brokers to resolve the conflict, it's unclear if they will get any closer to ending Syria's suffering.
Conversely, ML scores can also be used to judge the likelihood of a multiple alignment reflecting sequence evolution.
In these tests, each gene was compared against all the other gene trees and a usual value of p≤0.05 was used for the rejection of a given tree topology, suggesting that alignment reflects a non-vertical inheritance [22], [23].
In this case, the lower likelihood of the combined alignment reflects the improbability of a very long tree branch connecting two dissimilar clusters of sequences.
This effectively removes a codon from the alignment, reflecting the uncertainty in reconstructing the translated amino acid associated with the deletion.
Even though the maize genome survey reveals four putative loci coding for PA3 nucleases, the protein sequence alignment reflects that the tryptic peptide sequence exclusively matches with the maize protein code by gene LOC100282067 (Additional file 3: Figure S3).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com