The original article used a pre-release version of one of the annotation tools, snoStrip. During the proof reading, the snoStrip tool was released and published [1]. In this note, we bring the results of our original paper in accordance with the release version of snoStrip. Only the snoRNA annotation is affected, and no changes in conflicts of annotation is induced by the update. In summary, we found 621 high confident snoRNA loci using the combined snoStrip, BLAST, and Infernal-1.02/Rfam 10.1 annotation tools, compared to 638 high confident snoRNA loci when using the pre-release version of the snoStrip tool. The difference between this and the previous annotation is caused by the removal of 32 snoRNA loci, and the addition of 16 new loci, all of them annotated exclusively by the pre-release and the release versions of snoStrip, respectively. Two snoRNA loci (snoU2-30 and snoU2-19) from the previous version were combined to one locus (SCARNA9) in the current version.
The curation of the snoRNAs was also revisited. The newly annotated snoRNA loci were curated according to the methods outlined in the article, which results in 24 new curated snoRNAl loci, while 3 curated snoRNA loci where removed from the high confident set, and thus also from the curated set (these are syntenic pseudogenes in human and pig). SCARNA9, which was comprised of two different snoRNA annotations in the previous version, was curated as well.
As a final note, an rRNA incorrectly marked as curated in the previous annotation were removed from the curated set of genes in the current version.
The updated annnotation as well as a more detailed changelog is available on http://rth.dk/resources/rnannotator/susscr102/version1.03
snoStrip, is an annotation pipeline designed specifically for homology based annotation of snoRNAs, taken in to account factors beyond sequence and structure conservation. During the development phase a number of internal cutoffs and procedures were changed, which changed the results we originally used for the publication. New snoRNAs loci were introduced and others were removed. The original annotation was based in part on 513 snoStrip results. The release version changed this total to 504 loci, which is the result of the removal of 67 loci and the addition of 58 new ones. Based on hand curation we decided to keep 12 of the 67 loci, which cover two otherwise lost snoRNAs, SNORD89 and SNORD117, as well as four members of SNORD113, four members of SNORA70, and two members of SNORA22. That is 516 snoStrip-based annotations for pig in total.
The snoRNA annotation presented in the paper was a combination of high confident annotation based on snoStrip, BLAST, and Infernal 1.02/Rfam 10.1. In Table 2, we present the updated results of the homology based pipeline. After combination of the three methods we found 621 annotated snoRNA loci, compared to 638 snoRNA loci using the pre-release version. This change in the total number of annotated snoRNAS reflects that the release version of snoStrip has a larger overlap with Infernal/Rfam than the pre-release version, and therefore introduces fewer loci annotated exclusively by snoStrip. The number of conserved(syntenic) structured RNA loci and the number of structured RNA loci overlapping RNAz loci are also affected by the changes in the snoRNA annotation. The effect can be seen in the updated Tables 5 and 6. The curated annotation were updated as well as shown in Table 7.
RNA class | High
| |
Families | Loci | |
cisreg-elements | 31 | 139 |
lncRNA-loci | 58 | 58 |
miRNA | 321 | 359 |
ribozyme | 3 | 8 |
rRNA | 5 | 185 |
snoRNA | 209 | 621 |
snRNA | 10 | 1,030 |
tRNA | 51 | 810 |
Other | 7 | 153 |
Conflict | 9 | 11 |
Sum | 704 | 3,374 |
RNA class |
# loci | hg19 | RNAs conserved in N other organisms
| ||||
Syntenic | Conserved | Both | 1 | 5 | 15 | ||
cisreg-elements | 139 | 80 | 84 | 65 | 116 | 86 | 31 |
lncRNA-loci | 58 | 57 | 53 | 53 | 58 | 57 | 7 |
miRNA | 369 | 303 | 349 | 292 | 360 | 349 | 102 |
putative-miRNA | 155 | 121 | 25 | 20 | 65 | 25 | 1 |
ribozyme | 8 | 8 | 3 | 3 | 3 | 3 | 0 |
rRNA | 185 | 143 | 0 | 0 | 6 | 1 | 0 |
snoRNA | 621 | 457 | 268 | 225 | 406 | 286 | 42 |
snRNA | 1,030 | 674 | 24 | 13 | 119 | 26 | 4 |
tRNA | 810 | 549 | 274 | 199 | 389 | 284 | 14 |
other | 153 | 111 | 10 | 10 | 17 | 11 | 0 |
Conflict | 11 | 10 | 10 | 10 | 10 | 10 | 4 |
Sum | 3,539 | 2,513 | 1,100 | 890 | 1,549 | 1,138 | 205 |
RNA class | Annotation | RNAz overlap
| ||
Families | Loci | Families | Loci | |
cisreg-elements | 31 | 139 | 4 | 10 |
lncRNA-loci | 58 | 58 | 3 | 3 |
miRNA | 330 | 369 | 222 | 241 |
putative-miRNA | 135 | 155 | 14 | 16 |
ribozyme | 3 | 8 | 0 | 0 |
rRNA | 5 | 185 | 2 | 2 |
snoRNA | 209 | 621 | 57 | 74 |
snRNA | 10 | 1,030 | 9 | 20 |
tRNA | 51 | 810 | 36 | 154 |
other | 7 | 153 | 3 | 4 |
conflict | 9 | 11 | 4 | 6 |
sum | 848 | 3,539 | 354 | 530 |
# high confident loci | # curated loci | # pseudogenes | # loci,#pseudogenes subtracted | ||
cisreg-elements | 139 | 93 | 31 | 108 | |
lncRNA-loci | 58 | 0 | 0 | 58 | |
miRNA | 369 | 125 | 0 | 369 | |
putative-miRNA | 155 | 0 | 0 | 155 | |
ribozyme | 8 | 1 | 5 | 3 | |
rRNA | 185 | 2 | 182 | 2 | |
snoRNA | 621 | 289 | 251 | 370 | |
snRNA | 1,030 | 69 | 960 | 70 | |
tRNA | 810 | 0 | 0 | 810 | |
Other | 153 | 3 | 125 | 28 | |
Conflict | 11 | 8 | 0 | 11 | |
Sum | 3,539 | 590 | 1,555 | 1,984 | |
1. Bartschat S, Kehr S, Tafer H, Stadler PF, Hertel J: snoStrip: A snoRNA annotation pipeline. Bioinformatics 2014, 30(1):115–116.