snoSeeker Informations
Latest News:(27 January 2010)
We have predicted thousands of snoRNAs from next-generation deep-sequencing data from seven organisms(human, mouse, chicken, C.intestinalis, D.melanogaster, C.elegans and Arabidopsis) using snoSeeker. you can download predicted snoRNAs in deepBase database(http://deepbase.sysu.edu.cn)
snoSeeker results
The following data(human snoRNAs) has been published in the article[1].
1. Box C/D "orphan" snoRNA genes
2. Box C/D "guide" snoRNA genes
3. Box H/ACA "orphan" snoRNA genes
4. Box H/ACA "guide" snoRNA genes
Note:
(1)Now, you can download new results(human/vertebrate snoRNA database) [16 whole genome alignments(WGAs) to the human genome (hg18, Mar. 2006)] from snoSeeker(v 0.3)
Human/Vetebrate snoRNA database (snoSeeker v0.3)
(2)snoSeeker(version 0.3) can detect ~95% known C/D box snoRNA genes and >80% known H/ACA snoRNA genes in the human genomes. [ CDseeker Web-Server and ACAseeker Web-Server ].
(3)snoSeeker(version 0.3) prediect a large of novel putative snoRT(retrogene derived from sno/scaRNA) and isoform genes(duplication genes derived from known sno/scaRNA) in the human(vertebrate) snoRNA database.
these data were downloaded from UCSC Bioinformatics Site(http://www.genome.ucsc.edu)
Whole genome alignments(WGAs) of the following assemblies
to the human genome (hg18, Mar. 2006):
_ human Homo sapiens Mar 2006, hg18(HS)
_ mouse Mus musculus Feb 2006, mm8(MM)
_ rat Rattus norvegicus Nov 2004, rn4(RN)
_ dog Canis familiaris May 2005, canFam2(CF)
_ cat Felis catus Mar 2006, felCat3(FC)
_ horse Equus caballus Feb 2007, equCab1(EC)
_ cow Bos taurus Aug 2006, bosTau2(BT)
_ opossum Monodelphis domestica Jan 2006, monDom4(MD)
_ platypus Ornithorhychus anatinus Mar 2007, ornAna1(OA)
_ lizard Anolis carolinensis Feb 2007, anoCar1(AC)
_ chicken Gallus gallus May 2006, galGal3(GG)
_ frog Xenopus tropicalis Aug 2005, xenTro2(XT)
_ fugu Takifugu rubripes Oct 2004, fr2(FR)
_ tetraodon Tetraodon nigroviridis Feb 2004, tetNig1(TN)
_ stickleback Gasterosteus aculeatus Feb 2006, gasAcu1(GA)
_ medaka Oryzias latipes Apr 2006, oryLat1(OL)
_ zebrafish Danio rerio Mar 2006, danRer4(DR)
[1]Reference:
"snoSeeker: An advanced computational package for screening of guide and orphan snoRNA genes in the human genome"
Jian-Hua Yang, Xiao-Chen Zhang, Zhan-Peng Huang, Hui Zhou, Mian-Bo Huang, Shu Zhang, Yue-Qin Chen and Liang-Hu Qu
Nucleic Acids Res. Epub 2006 Sep 20;34(18):5112-23
NOTE!!!
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* HS is human, MM is mouse, RN is rat, CF is dog, BT is cow
* 5S is 5S rRNA, SSU is 18S rRNA, LSU is 28S rRNA, U1, U2... is snRNA
* Upstream/downstream is upstream/downstream identity
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Web page by Jian-Hua Yang(snoRNAseeker@gmail.com)
last modified: 2008/03/30 11:54:26
Orphan C/D snoRNAs part1 
16 whole-genome alignments (WGAs)