Strategies and Resources for the Identification of microRNAs in Non-model Plants

High-throughput sequencing of small RNAs is becoming increasingly affordable and accessible. The amount of data and information that has been generated over the last decade is enormous and continues to increase. Now the major constraint is the analysis and the organization of the data in order to extract useful biological information. Consequently, several software packages have been developed to analyze small RNA datasets and dedicated databases have been created to organize these data and information. However, these tools have limitations that need to be addressed. In this chapter, we present the most commonly used strategies and discuss their advantages and limitations.