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No amino acid or DNA sequence information in sequence databases was found for a fungal lactate dehydrogenase (LDH) isozyme.
Several studies pointed out the relevance of integrating secondary structure information in sequence analysis and phylogenetics, both in terms of phylogenetic resolution and of marker suitability for phylogenetic reconstruction at higher taxonomic-rank.
If the additional neighbor information in sequence is incorporated into the predictive model and better results can be expected.
In a benchmark dataset, we demonstrated that the inclusion of phylogenetic information in sequence reconstruction significantly improves the reconstruction accuracy compared with two standard approaches.
It is evident that integration of secondary structure information in sequence alignment and analyses (in the form of rRNA substitution models) will optimize rRNA phylogenies considerably.
The RP score was used in ESPERR (Evolutionary and Sequence Pattern Extraction through Reduced Representations) [ 10] to capture information in sequence alignments over seven vertebrate species.
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These challenges are further complicated by recent methodological developments that make it possible to use haplotype information in sequencing reads.
Therefore, we should choose analytical methods that are appropriate to the sequencing coverage and sample size in order to use haplotype information in sequencing reads.
Indeed, we detected a large amount of immunological status-specific information in sequence-independent clonal repertoire distributions.
Among others, Adami et al. [ 40] suggested to quantify the complexity by the amount of information in sequences (genomes).
However, since the functional diversity most likely accompanies sequence diversity, the quantification of information in sequences encounters the dichotomy of conservation and diversity.
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