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Table 1 Novel candidates of Human H/ACA snoRNA paralogs

From: Fast local fragment chaining using sum-of-pair gap costs

    annotated candidate regions in %  
sequence Identity fragments per chain number of chains snoRNABase Ensembl Eddy-BLAST-snornalib unknown
> 60% 1 286 37.8 94.4 84.3 6
  2 29 0 69 86.2 3
  ≥ 3 10 0 70 60 3
  all 325 33.2 91.4 83.7 12
> 70% 1 266 40.6 97.7 84.6 3
  2 21 0 85.7 95.2 0
  ≥ 3 8 0 87.5 75 1
  all 295 36.6 96.6 85.1 4
> 80% 1 233 46.4 98.7 85 1
  2 10 0 90 100 0
  ≥ 3 2 0 100 100 0
  all 245 44.1 98.4 85.7 1
  1. Summary of H/ACA snoRNA candidates in Homo sapiens including their fragment counts and their overlap with previous annotations, i.e., the snoRNABase, the set of snoRNAs and snoRNA pseudogenes from the Ensembl database and the Eddy-BLAST-snornalib in the UCSC RNAGenes track.
  2. The candidates were retrieved by combined use of BLAST (with options -W 8 -e 1e+20 -F F) and clasp (sum-of-pair gap costs with , , fragment scores according to the length of the BLAST hit, and a minimal required chain score of 30) with the entire set of Human H/ACA snoRNAs, annotated in the snoRNABase. Each candidate shows a highly conserved H box and ACA motif as well as high secondary structure conservation with two separate stem loop regions. Moreover, several different sequence identity scores in the ClustalW alignment to a known Human H/ACA snoRNA were required.