Insilico Finding Rnas In A Region

Question

[bari1]

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

[Pierre Lindenbaum]

cross posted on SO: http://stackoverflow.com/questions/12263141

[bari1]

sorry, i thought i posted on worng forum,

[Sean Davis]

You say that the region is not well-annotated in ensembl and UCSC. Have you looked at all of the potential EST and mRNA tracks?

From where did you get your 10Kb region? Is there a biological hypothesis that you are working with here?

[bari1]

so from UCSC and ensmebl it is intergenic region (of course annotated), but i donot find evidence for mRNA or ESTs on browsers. So i want an alternative to check if we could see any RNA / transcript. I mean UCSC and ensembl are the best to see what we have but are there any other ways also?

Answer 1

[JC]

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.