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They will provide small annotation datasets, identify new genes in an organism, further extend genic regions, and help with alternative splicing, especially in sequenced genomes.
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(c) Small RNA annotation frequency (percentage relative to total abundance) of clusters (distinct) and individual reads (abundance).
The small RNA annotation categories will be then identified, include microRNAs, repeat-associated RNA, non-coding RNA and mRNA degradation products.
A final small RNA annotation was obtained by following a priority rule: Genbank > Rfam > known miRNA > repeat > exon > intron > siRNA.
Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules.
For the analysis of the MCF-7, mES, and human CTCF data grouped into 'cancer' and 'normal' the data was parsed so that data points that intersected with known small RNA annotations, the 500 bp adjacent to TSSs, repeat masker annotations or Ensembl annotations less than 300 nucleotides were removed.
Small RNA annotations other than miRNA were downloaded from piRNABank (http://pirnabank.ibab.ac.in/) [54] and fRNAdb (http://www.ncrna.org/frnadb/) [55].
Summary of small RNA annotations from NJCMS1A and NJCMS1B.
This strategy allowed for some flexibility in small RNA annotations since repeat classes are often not distinct on a sequence level.
Because of the absence of small ncRNA annotations in S. ratti, the initial miRNA candidate list was filtered against ribosomal RNAs and compared with the Rfam database (version 11; Burge et al. 2013).
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