Question: new gene discovery
0
gravatar for songmm19900210
5.0 years ago by
songmm1990021020 wrote:

I want to blast my circRNAs which are identified by CIRI software to circRNAs which in circBase database(http://www.circbase.org/). how can i find new circRNAs from my identified circRNAs which are not in circBase database?
thanks!

blast rna-seq • 1.1k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by songmm1990021020
1
gravatar for songmm19900210
5.0 years ago by
songmm1990021020 wrote:

thanks Amitm, after blast with the fasta of the Circbase data, how to discoevey new circRNA? What is the criterion?

ADD COMMENTlink written 5.0 years ago by songmm1990021020

hi,

I'm sorry I do not have any experience in interpreting circRNAs. The identification using sequences was a generic step hence replied initially. Having said that there are a few low hanging fruits you could go for if you haven't already -

  1. Use BLAST E-value to select high-confidence candidates. (if you have too many to strt with)
  2. Assuming you are working with human/ mouse, ENCODE is a wonderful resource to test hypothesis. For your high-confidence candidates, go to the UCSC browser, turn on ENCODE tracks and see if you have sign of promoter upstream (like histone marks, TFBS etc.).
  3. Also you could check if the region has transcription signal in other ENCODE datasets as well
ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Amitm2.1k
1
gravatar for Amitm
5.0 years ago by
Amitm2.1k
UK
Amitm2.1k wrote:

hi,

Depending on the number of candidates you have, you could either use BLAST or bowtie. First you would need the fasta of the Circbase data, convert to a blast db or a bowtie index and then proceed.

If instead of fasta file, BED is available then use Galaxy: Extract Genomic DNA to get your db sequences first.

ADD COMMENTlink written 5.0 years ago by Amitm2.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2058 users visited in the last hour
_