Hello
I would like to scan some sequence data for ncRNA and I'm a little bit at a loss where to start as there are simply too many tools to chose from.
The most established one seems to be NCRNASCAN.
Is there a preferred ncRNA scan tool?
Many thanks
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Andrea_Bio •
A combination between tRNA Scan SE and RNAmmer would be good. Then, if you have other ncRNAs to find beside rRNA and tRNA then you can use predictors for those too. I think it's too difficult to predict ncRNAs as a whole group; it should be much easier to predict one class of them at a time.
i'm happy to do one groupa at a time. i want to scan an entire genome for each group for ab initio prediction but i can't find anything to do this, except for snoRNA
sorry, of course there is rnammer as you suggested but i would also like to find mirna genes.
Then, I suppose one of these packages would be good. http://www.bioinformatics.ca/links_directory/search/mirna
MicroInspector, RNAhybrid, ...
There are a number of tools. The choice depends on the nature of your input.
Is it a single sequence or a set of homologous (and aligned) sequences? Is it a short sequence (ie. <1k) or a long, genomic sequence?
Also, do want to do de-novo prediction or look for homologous RNAs?
For starters have a look at
Andreas
Thanks for answering. My input will be an entire genome for an organism. I would like to scan the genome to mine any potential RNA genes such as miRNA. The point behind this is I am looking for the consequences of SNPs in the genomes of 10-several hundred (don't know how many yet) individuals. I'm doing the typical ensembl consequence/polyphen route for SNPs in genes but it would be nice to try and say something about the SNPs in other areas too. I have just posted another question about this.
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just saw the mirna tag. are you exclusively looking for mirnas?
no, not specifically mirna. I thought i had added more tags than that.