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ESTs can, however, be aligned to small genes manually.

To investigate this further, predicted miRNA sequences were aligned to 773,450 small RNA sequences that were recently characterized from amputated and regenerating axolotl limbs (unpublished data).

In order to set the correct time delay, both the HIFU and laser fields were aligned to a small spherical target.

Then, we removed reads that were aligned to all known small RNAs using Bowtie (Langmead et al. 2009) allowing up to one mismatch ([-k 1 -v 1]).

Raw reads were aligned to a pseudometagenome (see small RNA methods) using Tophat v2.0.8 alignment options –read-mismatches 10 –edit-distance 12.

The small RNA libraries were aligned to the genome and canonical transposons, and then normalized with small nucleolar RNA-derived small RNAs, genic-endo-siRNAs and non-coding RNAs with respective heterozygous controls (Additional file 2: Table S1).

Fragments from each rice accession were aligned to each other for each small RNA locus.

After filtering out reads that are aligned to miRNAs, sn(o RNAs, small cytoplasmic RNAs, rRNA genes or known coding genes, we found 271,382 unique start positions on the positive strand and 309,051 unique start positions on the negative strand.

The fraction is calculated with respect to the size of the smaller network because in a global alignment all nodes of smaller network are aligned to nodes of larger network.

Raw data of small RNA reads from four corresponding small RNA libraries were aligned to the rice genome [ 41] by SMALT v0.5.7 with default parameters [ 62].

Small RNAs were aligned to NAT transcripts using SOAP [ 43].