Computational protocol: Identification and Comparative Profiling of miRNAs in an Early Flowering Mutant of Trifoliate Orange and Its Wild Type by Genome-Wide Deep Sequencing

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Protocol publication

[…] The potential targets of miRNAs were predicted using the psRNATarget program (http://bioinfo3.noble.org/psRNATarget/) with default parameters. The rules used for target prediction are based on those suggested , , with penalty scores ≤ 2 for mismatched patterns in the miRNA/mRNA duplexes. In addition, one mismatch was allowed in the region complementary to nucleotides 2–12 of the miRNA, but not at the cleavage site (nucleotides 10 and 11), and three additional mismatches were permitted between nucleotide positions 12 and 21, but no more than two consecutive mismatches within this region. The number of allowed mismatches at complementary sites between miRNA sequences and potential mRNA targets was no more than four, and no gaps were allowed at the complementary sites. Putative target genes were manually selected from these candidates based on their localization in citrus genome (http://www.phytozome.net/clementine.php). Functions of the predicted target genes were assigned manually according to the functions of the best hits from the BLAST search against the NCBI database. The hybridization energy of each miRNA-predicted target duplex (△G) was determined from the WMD3 output. […]

Pipeline specifications

Software tools psRNATarget, WMD
Databases Phytozome
Application Non-coding RNA analysis
Organisms Arabidopsis thaliana, Oryza sativa