I want to find novel and known RNAs and transcripts in a sequence of about 10 KB. What is the most easiest way using bioinformatics tools to start with if that sequence is not well annotated in ensembl and UCSC browsers? Does splices ESTs and RNA sequencing data one option? I am new to bioinformatics, your suggestions are useful for me.
Thanks in advance
If the region is not annotated by UCSC and Ensembl, it's because there are none or very little evidence from mRNA, EST and prediction systems. One alternative is to check with RNAseq data (look for the Illumina Body Map 2.0, it can be browsed with IGV or inside Ensembl) but the data will be noisy.