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In all 3 cases the deRIP sequences match best to the active transposons.
To this end, the coverage evenness score — equal to the number of unique reference positions matched by the first bases of reads extending past the breakpoint and any overlap or read-only junction bases — is recalculated based on the re-aligned reads that match best to each junction.
On page 11, you say, "The two members of Chlorobium phaeobacteroides show different affinities to other members of their own family: 53.2% of encoded proteins in C. phaeobacteroides strain BS1 match best to genus Prosthecochloris, whereas proteins in strain DSM 266 tend to best match the congener C. limnicola (39.0%) and the closely related genus Pelodictyon (32.4%)." First, 53.2% of what?
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The band at ∼30 kDa matched best to a 29 kDa salivary protein precursor (gi∣76589378).
The ∼38 kDa protein matched best to a salivary apyrase (gi∣10443907).
In total, 36,386 contigs matched best to proteins of the 10 most prevalent top-hit species, out of which 29,724 contigs (82%%) matched best to a protein sequence derived from a tick species (Fig. 1).
At the amino acid level, gene_2050O8-3 matched best to the rice putative protein Os03g02590 (peroxisomal membrane protein PEX11-1), displaying 87% homology over the entire length.
One type II cDNA sequence generated from RNA from melanocytes Benno matched best to an HML-2 locus in 3q12.3 (ERVK-5) but nevertheless displayed a relatively high number of six mismatches to that locus.
The two structures exhibit markedly distinct configurations in their N-terminal α-helical region (subdomain A), with the S. solfataricus MCM region matching best to the N-terminal domain configuration of Mcm4 and Mcm5.
From this population, we chose 4,068 SNPs that matched best to the Illumina SNP map of human chromosome 22 and had a minimum allele frequency of 0.05 or more.
This from an 80-year-old who had earlier told me he thought the two were "a lucky young match, best of love to 'em".
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com