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