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Question: new gene discovery
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gravatar for songmm19900210
5.0 years ago by
songmm19900210 • 20
songmm19900210 • 20 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
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modified 5.0 years ago • written 5.0 years ago by songmm19900210 • 20
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gravatar for songmm19900210
5.0 years ago by
songmm19900210 • 20
songmm19900210 • 20 wrote:

thanks Amitm, after blast with the fasta of the Circbase data, how to discoevey new circRNA? What is the criterion?
ADD COMMENT • link written 5.0 years ago by songmm19900210 • 20

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 REPLY • link modified 13 months ago by _r_am ♦ 32k • written 5.0 years ago by Amitm • 2.1k
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gravatar for Amitm
5.0 years ago by
Amitm • 2.1k
UK
Amitm • 2.1k 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 COMMENT • link written 5.0 years ago by Amitm • 2.1k
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