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deepBase: microRNA, other ncRNAs, deep sequencing data - annotate and discover microRNA and ncRNAs from deep sequencing data (Dec/01/2010 )

Dear All,

We introduce a novel platform/database, deepBase, which we have developed to annotate and discover small and long ncRNAs (microRNAs, siRNAs, piRNAs, snoRNAs ...) from next generation deep-sequencing data.

deepBase provides an integrative, interactive and versatile web graphical interface to evaluate miRBase-annotated miRNA genes and other known ncRNAs, explore the expression patterns of microRNAs and other ncRNAs, and discover novel miRNAs and other ncRNAs from deep-sequencing data. deepBase also provides a deepView genome browser to comparatively analyze these data at multiple levels.

deepBase is available at: http://deepbase.sysu.edu.cn/

deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res., 2010,38: D123-D130.
http://nar.oxfordjournals.org/cgi/content/full/gkp943

This is the first version of deepBase database. We look forward to your feedback.

Thanks!

-yjhua2110-

We also have mapped reads from deep-sequencing experiments to known microRNAs downloaded from miRBase and developed a variety of interfaces and graphical visualization to view these mapped reads. You can retrieve a list of microRNAs and list of variants and their read counts and isomiRs...

Web interfaces to view mapped reads associated with known microRNAs as follows:
(1) http://deepbase.sysu.edu.cn/browseNasRNA.php
(2) http://deepbase.sysu.edu.cn/browseExpress.php

http://deepbase.sysu.edu.cn/images/heatmap.png

-yjhua2110-