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deepbase: microRNAs and other ncRNAs, deep sequencing data

deepbase: microRNAs and other ncRNAs, deep sequencing data - Bioinformatics

deepbase: microRNAs and other ncRNAs, deep sequencing data - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 12-02-2010, 01:30 PM
Pipette Filler
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Default deepbase: microRNAs and other ncRNAs, deep sequencing data



Dear All,

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

deepBase is available at: [Only registered users see links. ]

deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res., 2010,38: D123-D130.

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

Thanks!

Last edited by rnaworld2110; 12-08-2010 at 04:50 PM.
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Old 12-07-2010, 11:26 PM
Pipette Filler
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Default Re: deepbase: microRNAs and other ncRNAs, deep sequencing data

please tell me a proper step on how to find a primer and promoter sequence in Arabidopsis and tomato and how can I choose the best sequences
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Old 12-08-2010, 04:39 PM
Pipette Filler
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Default Re: deepbase: microRNAs and other ncRNAs, deep sequencing data

Quote:
Originally Posted by ifhmn View Post
please tell me a proper step on how to find a primer and promoter sequence in Arabidopsis and tomato and how can I choose the best sequences
Maybe, the PlantProm (a database of plant promoter sequences) will be useful for your research:
PlantProm website: mendel.cs.rhul.ac.uk/mendel.php
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Old 01-19-2011, 12:44 PM
Pipette Filler
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Default mapped reads associated with known microRNAs

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) [Only registered users see links. ]
(2) [Only registered users see links. ]

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data , deep , deepbase , micrornas , ncrnas , sequencing


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