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The vast majority of characterized RLEs reside in the 5' or 3' untranslated regions (UTRs) of their transcripts, although a few have been mapped to protein coding regions [5].
The gene lists were then mapped to protein lists using our in-house mapping tools.
Genes were mapped to protein clusters from [ 5] and from them to T. reesei.
DEGs were subsequently mapped to protein interaction maps for further analysis.
All mutations were then mapped to protein sequences and thence to structure as described previously [ 19].
The remaining mitochondrial reads mapped to protein coding genes, rRNA and intergenic regions.
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We also masked the repeat sequences using Exonhunter (http://lifecenter.sgst.cn/schistosoma/en/schistosomaCnIndexPage.do) and RepeatMasker programs [26] (http://www.repeatmasker.org), and ones mapped to protein-coding exons.
The data indicated that about 16 21% of the small RNAs matched with rRNAs, tRNAs, snRNAs and snoRNAs (Figure 2C and 2D), ∼24% mapped to repeat sequences, including transposons and retrotransposons, and ∼1.2% mapped to protein-coding exons.
The best SNP signal in each gene was mapped to proteins in a human protein interaction network and their significance of clustering in functional network modules was evaluated.
Additional file 7: Number of PHAS loci mapped to protein-coding genes.
In total, over 136 million reads were mapped to protein-coding genes.
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