Table 3

Number of remaining input sequences from each step of target identification on the previously reported miRNA-associated target sequences of Arabidopsis

Step/Number of remaining sequences

Default settings

Customized settings


Number of input sequences

434

434


1. Sequence loading

434

434


2. Target scanning*

410

430


3. miRNA-target folding

410

430


4. Target annotation**

UniProtKB/Swiss-Prot

400

405


UniProtKB/TrEMBL

406

427


* The default and customized binding scores for target scanning were ≤ 4 and ≤ 6, respectively.

** The default and customized BLASTX E-values for target annotation were 1E-20 and 1E-5, respectively. Both protein databases were prepared with plants only.

Numnark et al. BMC Genomics 2012 13(Suppl 7):S16   doi:10.1186/1471-2164-13-S7-S16

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