## Description

This track shows the location of non-protein coding RNA genes and pseudo-genes.

Feature types include:

- tRNA: Transfer RNA (or pseudogene)
- rRNA: Ribosomal RNA (or pseudogene)
- scRNA: Small cytoplasmic RNA (or pseudogene)
- snRNA: Small nuclear RNA (or pseudogene)
- snoRNA: Small nucleolar RNA (or pseudogene)
- miRNA: MicroRNA (or pseudogene)
- misc_RNA: Miscellaneous other RNA, such as Xist (or pseudogene)

## Methods

#### Eddy-tRNAscanSE (tRNA genes, Sean Eddy):

tRNAscan-SE 1.23 with 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, with 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 with P <= 0.001.

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

WUBLASTN 2.0, with 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] with options: "-kap -cpus=1 -wordmask=seg -W=8 -E=0.01 -hspmax=0 -B=50000 -Z=3000000000". Exceptions to this are:

- Large ncRNAs (LSU & SSU rRNA, H19, Xist): change "-W=11"; addition "-maskextra=50". Xist contains repetitive elements and was masked with RepeatMasker, Library version 6.8.
- microRNAs: "-kap -cpus=1 -S=70 -hspmax=0 -B=100" replaces all above parameters.

The score field contains the BLASTN score. Used 41 unique miRNAs, 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". An exception to this is: all miRNAs consist of 16-26 bp 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.

## Credits

These data were kindly provided by Sean Eddy at Washington University.