How to proceed for Annotation and Characterization of novel miRNA

[csmbiotech]

We have sequenced miRNA of bubaline/buffalo leukocytes. Some novel miRNAs have been obtained.

One example file has been attached.

We are now blasting each of the novel miRNA sequence against the miRBase which has yielded miRNA sequences from other animal species like human, mice etc (E-value as small as 0.0001). We are then opening:

1. Interaction explorer (http://www.informatics.jax.org/interaction/explorer)*

2. Gene Ontology Classifier

3. KEGG

Please advice what should be the pipeline to annotate the novel miRNA*in a species like buffalo where Chromosome wise genomic data are not available?

How to proceed for Annotation and Characterization of novel miRNA?.

[diego diaz]

You could use Rfam. The difference between miRBase and RFam is that in RFam both the sequence and secundary structure are considered to search related RNAs.

Also, you could use RNAFold to predict RNA secondary structure.