This track shows conserved non-coding regions predicted by RNAz [1,2].
This track is prepared to give interoperability with the functional RNA database [3] v3.0.
Short sequences (shorter than 30nt) are aligned to genome by SeqMap [4] with 0 mismatch, no-gap and no-repeat.
Other sequences are aligned to genome by BLAT [5] with identity>=99, coverage>=90 and no-repeat.
And limit results to predicted positions by RNAz.
[1] Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF.
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome.
Nat Biotechnol. 2005 Nov;23(11):1383-90.
[2] Washietl S, Hofacker IL, Stadler PF.
Fast and reliable prediction of noncoding RNAs.
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9. Epub 2005 Jan 21.
[3] Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K.
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.
Nucleic Acids Res. 2007 Jan;35(Database issue):D145-8.
[4] Jiang H, Wong WH
SeqMap: mapping massive amount of oligonucleotides to the genome.
Bioinformatics. 2008 Oct 15;24(20):2395-6. Epub 2008 Aug 12.
[5] Kent WJ.
BLAT--the BLAST-like alignment tool.
Genome Res. 2002 Apr;12(4):656-64.