Dear All,
We identified 857 novel snoRNAs, as well as 1032 known snoRNAs from 370 million sequence reads generated by 237 small RNA sequencing data (ENCODE and GEO) using snoSeekerNGS and provided the comprehensive catalog of human snoRNAs/snoRNAome and snoRNAs of other species such as mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana.
We also constructed the comprehensive expression pattern of human snoRNAs in various tissues and cell lines using small RNA sequencing data from ENCODE and GEO in deepBase and deepBase v2.0. Many of them are tissue-specific or cancer-specific.
All novel and known snoRNAs can be downloaded from our deepBase download Center.
SnoSeekerNGS is freely available from the following URL: http://deepbase.sysu.edu.cn/SnoSeekerNGS.php. Choose the appropriate platform for a binary distribution or a graphical user interface distribution.
deepBase and deepBase v2.0 have been published in Nucleic Acids Res. on 2010 Jan and 2016 Jan. deepBase paper:
- deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res. 2010 Jan;38(Database Issue): D123-D130.
- deepBase v2.0: Identification, Expression, Evolution and Function of Small RNAs, LncRNAs and Circular RNAs from Deep-sequencing Data. Nucl. Acids Res. (04 January 2016) 44 (D1): D196-D202
Hey SnoSeekerNGS devs - in case you're still around, is there any chance this package is still maintained? The binary files that are on the website are not very usable (for linux at least). Any chance you have a compilable version? Thanks!!!
This user has not logged in to Biostars for over a year so think of a plan B, just in case.
Thanks GenoMax, are you a bot/AI or just omnipresent? (which is almost the same)
None of the above :-) If you click on the user name you can see when they last logged in.