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Candidates were processed from annotated alternative splicing events (Wang et al).
Initially, only the "BothSafe" candidates were processed through steps 4 7.
The ESTs were aligned to all the sRNA sequences from C. trifoliata, and then the miRNA candidates were processed by miRCat http://srna-tools.cmp.uea.ac.uk/; [ 43]), using default parameters, to generate the secondary structures.
To study potential va-miRNAs precursor sequences, all sRNAs from grapevine were aligned against the grapevine genome and then the miRNA candidates were processed by miRCat http://srna-tools.cmp.uea.ac.uk/[ 60], using default parameters, to generate the secondary structures.
To study potential Vvi-miRNAs precursor sequences, all sRNAs from grapevine were aligned against the grapevine genome and then the miRNA candidates were processed by miRCat (http://srna-tools.cmp.uea.ac.uk/) [ 33], using default parameters, to generate the secondary structures (Additional file 1).
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Two candidates are processed at a time via QPBO graph-cut, and the candidate optimizing the MAP solution is selected.
To localize EPSCs, the occurrence time candidates are processed from earlier to later along the original data trace in the following manner.
The remaining 5 of 17 failed to be detected suggesting that these particular miRNA candidates are processed inefficiently in HEK293 cells, undetectable due to technical limitations or simply not valid miRNAs.
A total of 192 candidate SNPs were processed using the Illumina GoldenGate platform and 132 markers were successfully genotyped (Table S2).
Digital photographs of the candidate greeting voters were processed on the bus and circulated immediately.
Pairs with the absolute spearman correlation higher than 95% of random pairs were retained as candidate pairs, which were processed to infer the transcriptional interactions.
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