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Since one Alu-derived read can not be mapped specifically to any genomic Alu sequence, this possibility can not be ruled out.
A large percentage of these duplications (82%) can be mapped specifically to the R. oryzae lineage or to the lineage preceding the separation of R. oryzae and Phycomyces blakesleeanus and thus are specific of Zygomycota species.
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Of the 115 contigs, 48 were mapped specifically to chromosome 26, and 67 contigs also mapped to other regions of the genome.
Many differentially expressed genes were annotated as enzymes likely to be relevant to digestion or metabolism, or their expression had previously been mapped specifically to larval or adult midgut by the Fly Atlas microarray project (Chintapalli et al., 2007).
This was confirmed by PCR and sequencing, and mapped specifically to the 3′-most R4 region.
Separation measures how specifically the clustering can be mapped to the MIPS gold standard set without cross-complex contamination.
Reads from both libraries were mapped strand-specifically to quantify miRNA and miRNA* expression using Blastn (e-value < 0.0001, 100% identity, S = 1 for miRNA and S = 2 for miRNA*).
Of all the reads, over 6.5 to 14 million reads could be mapped from each sample to mRNA specifically (Additional file 4).
Furthermore, targets of the specifically expressed miRNAs were mapped to gene function databases, pathway databases, and regulatory networks.
Reads ranging from 20 to 24nt from both sRNA libraries were mapped strand-specifically against all identified possible targets for all cassava miRNAs to quantify possible transient siRNAs and mRNA fragments generated by miRNA-mediated cleavage (e-value < 0.0001, 100% identity, S = 1 for miRNA and S = 2 for miRNA).
We obtained 45 bp reads, the majority of them are paired end (i.e. containing reads from both the 3′ and 5′ end of a ∼250 bp fragment, see Table 1), that were mapped to a transcriptome reference sequence set specifically constructed for PE RNA-seq (see Materials and Methods).
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