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Given that the meta-RNA program uses universal HMM models (one each for Bacteria and Archaea) for predicting 16S rDNA fragments, it is expected that the meta-RNA program will miss such 16S rDNA sequences having deviant sequence architectures.
Similar(59)
Because in general the TEP species tended to each be reciprocally monophyletic with similar topology as in other gene regions, and at least 10 individuals from each of these taxa remained after the 8 sequences are removed, we excluded the deviant sequences from further analysis at this locus.
Of the 59 deviant sequences, 11 have alterations in two helices and 4 lack a helical segment.
These deviant sequences (but not the majority of the sequences with the same species annotation) were excluded from the analysis of intra- and interspecific similarity.
Third, the PCA of base composition revealed that the slightly GC-rich sequences from the Doliolum species are the closest in composition among tunicates to the deviant aplousobranch sequences, another potential cause of the observed phylogenetic artefact.
We then measured MMN to the same deviants in a linked sequence where deviants were paired duration deviants followed an intensity change and spatial deviants followed a frequency change.
Clean and reverberant speech files were delivered in a pseudo-randomized order, forcing at least one standard stimulus to be presented between successive deviants, in sequences of 100 trials.
MMN was elicited to rare (p = .125) physical "deviants" amongst a sequence of highly probable (p = .875) "standard" sounds.
They presented two sequences of deviant (target) and standard (non-target) tones to the subject.
Sequences containing deviant instruments were excluded from further analysis (because they were only employed to devise a task for the subjects, see also above).
Sequences with deviant amino acid composition were excluded to reduce the noise relative to the phylogenetic signal in the dataset.
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