An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs.MicroRNA are small non-coding RNAs that post-transcriptionally regulate the expression levels of messenger RNAs.  ComiR is a web tool realized to predict the targets of a set of microRNAs, starting from their expression profile.  ComiR was trained with the information regarding binding sites in the 3'utr region, by using a reliable dataset containing the targets of endogenously expressed microRNA in D. melanogaster S2 cells.  This dataset was obtained by comparing the results from two different experimental approaches, i.e., inhibition, and immunoprecipitation of the AGO1 protein--a component of the microRNA induced silencing complex.In this work, we tested whether including coding region binding sites in ComiR algorithm improves the performance of the tool in predicting microRNA targets.  We focused the analysis on the D. melanogaster species and updated the ComiR underlying database with the currently available releases of mRNA and microRNA sequences.  As a result, we find that ComiR algorithm trained with the information related to the coding regions is more efficient in predicting the microRNA targets, with respect to the algorithm trained with 3'utr information.  Finally, we propose to upgrade the existing ComiR web-tool by including the coding region based trained model, available together with the 3'utr based one.
ComiR
An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs.MicroRNA are small non-coding RNAs that post-transcriptionally regulate the expression levels of messenger RNAs.  This dataset was obtained by comparing the results from two different experimental approaches, i.e., inhibition, and immunoprecipitation of the AGO1 protein--a component of the microRNA induced silencing complex.In this work, we tested whether including coding region binding sites in ComiR algorithm improves the performance of the tool in predicting microRNA targets.  As a result, we find that ComiR algorithm trained with the information related to the coding regions is more efficient in predicting the microRNA targets, with respect to the algorithm trained with 3'utr information. 
ComiR algorithm
We focused the analysis on the D. melanogaster species and updated the ComiR underlying database with the currently available releases of mRNA and microRNA sequences. 
ComiR underlying database
We focused the analysis on the D. melanogaster species and updated the ComiR underlying database with the currently available releases of mRNA and microRNA sequences. 
microRNA sequences