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We thank Andrew Spiers, Rob Edwards, Dave Ussery, Chris Taylor, Peter Sterk, Mike Allen, Anil Wipat, Alice MorningStar, Lisa Crossman, Jack Gilbert and Sarah Turner for critical reading of the manuscript and Keith Keller for mapping of unique identifiers for use in the MicrobesOnline database [27].
First, mapping of unique reads to the potential NAGNAG alternative splicing sites in human lincRNA demonstrated existence of NAGNAG alternative splicing in lincRNA (Table 1).
After mapping of unique DNA fragments (enriched by DNA bound by TF molecules) onto the genome, the DNA fragment sequences, extended further up to ~200 bp, are clustered by their overlapping sub-sequences and mapped onto the genome.
To address this we examined separately the mapping of unique L1Hs and L1PA reads to intronic and intergenic regions, and found very similar tumor-associated increases in the abundance corresponding to both regions (Additional file 1: Figure S15).
The paucity of EC assignments limits this aspect of analysis but the mapping of unique sequences to the KEGG metabolic and other pathways still presents some useful perspectives on the metabolic, protein folding and degradation and cellular repair emphasis of desiccating cells.
We have recently explored the use of photodissociation methods, including infrared multiphoton dissociation (IRMPD) and ultraviolet photodissociation (UVPD), for the characterization of lipid A. UVPD led to the production of an impressive array of diagnostic fragment ions that facilitated mapping of unique modifications.
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The mapping of unique-mapped and multi-mapped reads to the genome identified both sequences related to TE piRNAs (i.e., reads mapping to piRNA clusters and TEs referred to as piRNA reads), as well as sequences corresponding to cellular mRNAs.
The mapping rate of unique reads (uniquely mapped reads/total reads × 100%) varied widely between the accessions, from 62.3 to 84.8% (Fig. 4).
We show how a map of unique seed regions can be used to generate tracts of interest.
Figures 8 and 9 illustrate the final enrichment map of unique human-specific and conserved blood-selective and brain-selective functions, respectively.
Electron crystallography and single-particle EM rely on averaging and thus require many identical copies of the same molecule; however, electron tomography can be used to obtain 3D density maps of unique objects in situ 30).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com