Description

This track shows where non-protein coding RNA genes and pseudo-genes are located. This data was kindly provided by Sean Eddy at Washington University.
Feature types:

Methods

Eddy-tRNAscanSE (tRNA genes, Sean Eddy)

tRNAscan-SE 1.23 w/ default parameters. Score field contains tRNAscan-SE bit score; >20 is good, >50 is great.

Eddy-BLAST-tRNAlib (tRNA pseudogenes, Sean Eddy)

WUBLAST 2.0, w/ options "-kap wordmask=seg B=50000 W=8 cpus=1". Score field contains % identity in BLAST-aligned region. Used each of 602 tRNAs and pseudogenes predicted by tRNAscan-SE in the human oo27 assembly as queries; kept all nonoverlapping regions that hit one or more of these w/ P <= 0.001.

Eddy-BLAST-snornalib (known snoRNAs and snoRNA pseudogenes, Steve Johnson)

WUBLASTN 2.0, w/ options "-V=25 -hspmax=5000 -kap wordmask=seg B=5000 W=8 cpus=1". Score field contains BLAST score. Used each of 104 unique snoRNAs in snorna.lib as a query. Any hit >=95% full length and >=90% identity is annotated as a "true gene". Any other hit with P <= 0.001 is annotated as a "related sequence", and interpreted as a putative pseudogene.

Eddy-BLAST-otherrnalib

(non-tRNA, non-snoRNA noncoding RNAs with Genbank entries for the human gene.) WUBLASTN 2.0 [15 Apr 2002] w/ options: "-kap -cpus=1 -wordmask=seg -W=8 -E=0.01 -hspmax=0 -B=50000 -Z=3000000000"
Exceptions: Score field contains BLASTN score. Used 41 unique miRNA, and 29 other ncRNAs as queries. Any hit >=95% full length and >=95% identity is annotated as a "true gene". Any other hit with P <= 0.001 and >= 65% identity is annotated as a "related sequence". Exceptions: all miRNAs consist of 16-26bp sequences in Genbank and are only annotated if 100% full length and 100% identity. miRNAs consist of Let-7 from Pasquinelli et al., Nature (2000) 408:86; 40 from Mourelatos et al., Gene & Dev (2002) 16:720.