Question: Insilico Finding Rnas In A Region
0
gravatar for bari1
19 months ago by
bari140
bari140 wrote:

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

ADD COMMENTlink written 19 months ago by bari140

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

ADD REPLYlink written 19 months ago by Pierre Lindenbaum58k

sorry, i thought i posted on worng forum,

ADD REPLYlink written 19 months ago by bari140

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?

ADD REPLYlink written 19 months ago by Sean Davis15k

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?

ADD REPLYlink written 19 months ago by bari140
0
gravatar for JC
19 months ago by
JC4.8k
Seattle
JC4.8k wrote:

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.

ADD COMMENTlink written 19 months ago by JC4.8k
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