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Briefly, using the Perl programming language, counts for all kmers between two sets of sequences are tallied and evaluated for significant over-representation between the sets using a Z-test, and all kmers with Bonferroni-adjusted p-value < 0.01 were clustered and aligned into groups of motifs.
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They are divided into (or "aligned into", to use phonology jargon) three vowel harmony groups by a parameter called ATR (advanced tongue root); the groups are −ATR, +ATR, and neutral.
The sequences must then be aligned into evolutionarily conserved groups to compare the sites across species.
To cluster the aligned contigs into groups, we used bedtools [ 53] setting the distance threshold parameter at 0. For transcripts that did not align with any similarity to bat, primate, or nt BLAST databases, we applied a series of filters to select for the coding transcripts to be validated.
The complex cations are aligned into 1D supramolecular chains through the NH⋯Cl hydrogen bonding between the amine group of the quinolinone ligand and the chlorido ligand of the adjacent complex anion.
The myristoyl group was taken from PDB entry ; 1qa5 and manually aligned into the bilayer using PyMol.
Thus, just after sonication, the layers aligned into dendritic architectures via hydrogen bonding and the ion-dipolar interactions between the carboxyl groups and water molecules [80].
The nations of mankind are loosely aligned into three factions.
Sequences were aligned into families according to sequence homology.
FATCAT breaks the proteins to be aligned into fragments eight residues long (aligned fragment pairs [AFPs]).
The resultant sequences were grouped into clusters using a customized program (Cluster 6) based on identity (95% identity, 64 word size) and aligned into contiguous sequences (contigs) using the CAP3 sequence assembly program [ 78].
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CEO of Professional Science Editing for Scientists @ prosciediting.com