PAREsnip

[…] and antisense tags. The tags mapped to cDNA or mRNA sequences were then used to predict cleavage sites. The pure reads with 20 and 21 nucleotides were used to identify potentially cleaved targets by PAREsnip (http://srna-workbench.cmp.uea.ac.uk/tools/paresnip/) and CleaveLand 3.0 (http://sites.psu.edu/axtell). The targets predicted were classified into five categories (0, 1, 2, 3 and 4) according […]

[…] of the sequence was a single base. Next, distinct tags that perfectly matched mulberry cDNA or mRNA sequences by SOAP2.20 based on Genbank of NCBI (http://www.ncbi.nlm.nih.gov/), the known miRNAs by PAREsnip from miRBase (miRBase21.0: http://www.mirbase.org/), or miRNAs identified in other studies [,] were used to analyze miRNA-mRNA pairs. Alignments were then scored according to a previously des […]

[…] sing PatMaN through the UEA sRNA workbench (). Predictions of tRF target genes were made using the psRNA-Target () using a mRNA/tRF pair scoring cutoff of E ≤ 5. PARE-seq libraries were analyzed with PAREsnip through the UEA sRNA workbench (). The default high stringency settings were used, removing the t/rRNA filtering step. Protein coding genes and TEs identified through this method were further […]

[…] o AGO protein-complexes. Most of them could be loaded onto AGO1, which has an important role in antiviral silencing (Peláez and Sanchez, ). The interactions detected for conserved microRNAs using the PAREsnip algorithm and the degradome data were mainly validated interactions. For this reason, the amount of interactions detected between ArT-sRNAs and host transcripts suggests that ArT-sRNAs may he […]

[…] mismatches allowed on the 10th and 11th nucleotides of mature miRNAs where the splice site on miRNA targets generally occurs in degradome analysis. Potential miRNA targets with a P-value of < 0.05 by PAREsnip software were retained, and T-plot figures were drawn. All target sequences were categorized into five classes based on the abundance of degradome tags indicating miRNA-mediated cleavage. The […]

[…] g unannotated sequences were mapped to the reference genes (cDNA) of the C. sinensis genome (Xu et al., ) by SOAP2 (Li et al., ). The reads mapped to cDNA_sense were used to predict cleavage sites by PAREsnip (version 2.3; Folkes et al., ). The cleaved target transcripts were categorized into five classes based on the abundance of degradome reads indicative of miRNA-mediated cleavage. Category 0 c […]