All possible predicted RNA in mm9 genome
Seeking a database of all possible predicted RNA in the entire mm9 genome. mfold will do this but has a 9000 base limit.
I'm sure I can't be the first one who would like to browse the output of all possible predicted RNA structures from the genome including intronic sequences as a database where I can filter on thermodynamic properties of the predicted molecule.
Thanks in advance!
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Ensembl's version: ftp://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/cdna/
The cDNA file will have the sequences for both protein coding genes and otherwise. Our ncRNA will have non-coding transcript sequences only. The GTF will give you the gene sets (both coding and non coding genes). Check our doc on annotation of ncRNAs for more details.
To state another way what I meant:
A whole genome in-silico prediction of all possible sub-sequences of DNA that would form a secondary structure.