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Surrogate datasets were created by randomly shuffling the ISIs of the measured sequence.
We measured sequence variation in terms of, the average of p(1 − p) within a window.
We measured sequence similarity and divergence across each BAC using the phylip program dnadist, implemented in the Mobyle online bioinformatics server [ 106].
Here, we measured sequence conservation for each amino acid site by calculating a normalized evolutionary rate from a global multiple species alignment in UCSC genome browser [ 21].
Third, we measured sequence divergence within duplicate gene groups, using a homology-based clustering coefficient, which increases inversely to sequence divergence.
To test whether coiled-coil regions carry phylogenetic information, we measured sequence conservation of coiled-coil regions and compared it with globular domains in a collection of over 2,000 orthologous groups of metazoan proteins.
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Phylogenetic information was obtained by comparing the measured sequences to the sequences deposited in the GenBank DNA database by using the BLAST algorithm [48].
We measured sequencing error in the newly available low-coverage (∼2×) genome by comparing them with corresponding "comparative-grade" sequences from the ENCODE project [23], [24] (Table 1).
(II) Experimental thermodynamic parameters and error limits for newly measured sequences.
The coefficient of correlation for all measured sequences was at least 0.99.
Rarefaction analysis showed that the OTUs of 36 samples gradually increased with the increase of the number of measured sequences.
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CEO of Professional Science Editing for Scientists @ prosciediting.com