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.