SnoRNA prediction software

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The small nucleolar RNAs (snoRNAs) represent an abundant group of small non-coding RNAs (ncRNAs) in eukaryotes.[1] With the exception of RNase MRP, all the snoRNAs fall into two major families, box C/D and box H/ACA snoRNAs, on the basis of common sequence motifs and structural features. They can be divided into guide and orphan snoRNAs according to the presence or absence of antisense sequence to rRNAs or snRNAs. Recently, thousands of novel snoRNAs were identified from small RNA sequencing datasets in human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana using snoSeekerNGS program.[2][3]

snoRNA prediction software[edit]

Name Description type Link References
snoSeeker snoSeeker includes two snoRNA-searching programs, CDseeker and ACAseeker, specific to the detection of C/D snoRNAs and H/ACA snoRNAs from four human–mammal whole-genome alignment (WGA) sequences. Recently, snoSeeker has been used to scan human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana sequences and identified thousuands of snoRNA genes from small RNA deep-sequencing (next generation sequencing) data.[2] webserver, standalone [1] [3]
snoScan A computational screen for C/D box methylation guide snoRNAs in a genomic sequence. webserver, standalone [2] [4]
snoGPS Search for H/ACA snoRNA genes in a genomic sequence. web-server, stand-alone [3] [5]
SnoReport Computational identification of snoRNAs with unknown targets. stand-alone [4] [6]
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References[edit]

  1. ^ Kiss T. (2002). "Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions.". Cell. 109 (2): 145–8. doi:10.1016/S0092-8674(02)00718-3. PMID 12007400. 
  2. ^ a b Yang JH, Shao P, Zhou H, Chen YQ, Qu LH (2010). "deepBase: a database for deeply annotating and mining deep sequencing data.". Nucl. Acids Res. 38 (Database issue): D123–130. doi:10.1093/nar/gkp943. PMC 2808990free to read. PMID 19966272. 
  3. ^ a b Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH (2006). "snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.". Nucleic Acids Res. 34 (18): 5112–5123. doi:10.1093/nar/gkl672. PMC 1636440free to read. PMID 16990247. 
  4. ^ Lowe, T. M.; Eddy, S. R. (February 1999). "A Computational Screen for Methylation Guide snoRNAs in Yeast". Science. 283 (5405): 1168–1171. Bibcode:1999Sci...283.1168L. doi:10.1126/science.283.5405.1168. PMID 10024243. 
  5. ^ Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM (2004). "Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome.". Nucleic Acids Res. 32 (14): 4281–96. doi:10.1093/nar/gkh768. PMC 514388free to read. PMID 15306656. 
  6. ^ Hertel J, Hofacker IL, Stadler PF (2008). "SnoReport: computational identification of snoRNAs with unknown targets.". Bioinformatics. 24 (2): 158–64. doi:10.1093/bioinformatics/btm464. PMID 17895272.