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The different parameters are estimated by using the Maximum Expectation of joint Likelihood criterion.
By showing no substantial difference with this baseline, our method roughly reaches the maximum expectation of accuracy in this experiment.
The maximum expectation of 3.5 was applied in the target search.
We ran the known miRNAs, new miRNAs and 19 23 nt smRNAs against the TSS with a maximum expectation of 5 and an hspsize (which is the length of the region used to score the complementarity between the miRNA and its target) equal to the length of the smRNA (to ensure that the entire sequence of the smRNA is considered by the scoring algorithm).
Similar(56)
The maximum expectations of 3.0 and the target accessibility-allowed maximum energy to unpair the target site of 50 were applied.
A minimal ProteinProspector protein score of 15, a peptide score of 15, a maximum expectation value of 0.1, and a minimal discriminant score threshold of 0.0 were used for initial identification criteria.
Sequence alignments were performed using standalone MegaBLAST [ 53] obtained from NCBI, BLAST FTP site [ 54] with default settings except for a window size of 16 (-W 16), maximum expectation value of 1 × 10-10 1e-010-010) alignmentment output (-D 3).
We mapped reads back to contigs using a BLASTN search (version 2.2.23), where 70%% of a read was required to align to a contig with a maximum expectation value of 10−30, and searched for reads that spanned some or all of the putatively transferred ORF and its neighbors.
The potential targets of conserved miRNA families were identified by a search in the website http://bioinfo3.noble.org/psRNATarget/, with the following settings applied: transcript/genomic library A. thaliana TAIR7 cDNA [25/04/2007 release]; range of maximum expectation 1-5; range of maximum circles 1-3; range of central mismatch for translational inhibition 9-11 nt.
A maximum expectation value of 0.1 was employed as a threshold for peptide identifications.
Because the chip covers 31 099 genes, the maximum expectation value of false positives for each comparison is 3.1 (=31 099 × 0.01 x 0.01).
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