Transcript 2619_sRNASlides2012short

project date 20/07/2012
The sRNA Workbench
Matthew. B. Stocks
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PROJECT AIMS
Based on original algorithms developed for the web based UEA
sRNA Tools
Moxon et. al. (2008)
Easy to use
•
Designed to be used by biologists with limited access to
bioinformatics support, perhaps on a desktop computer (but is
extendable to servers or high performance clusters)
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Cross platform support
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To allow multiple analysis techniques from within a single
program through the use of an MDI (Multiple Document
Interface)
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Performance improvements, Speed, Memory
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Still accessible through the command line
Code maintainability
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WHAT WE ALREADY OFFER
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HELPER TOOLS
Adapter Removal
Removes 3’ and/or 5’ adaptors from raw highthroughput sequence data
FASTA or FASTQ
Provides sRNA length distribution
Filter
Filters sRNA sequences from high-throughput data
according to user-defined criteria
Sequence Alignment
Aligns sRNA Sequences to a Reference Genome or
other long read file
DEFAULT STYLES
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ANALYSIS TOOLS
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miRCat
•miRCat (micro RNA Categorisation)
Moxon et. al (2008) Stocks et. al. (2012)
Identify novel miRNAs in high-throughput sequence data
Identify known miRNAs found in miRBase in result set
Griffiths-Jones (2010)
View miRNA statistics
One click viewing of the predicted miRNA as they appear on the
genome
One click viewing of miRNA pre-cursor secondary structure plot
Concurrency....
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miRCat threading
sRNA
sRNA
sRNA
CPU
Core
CPU
Core
Thread Pool:
FIFO data structure (Queue)
First sequence added to the list (First In) is the first item
processed (First Out)
sRNA
sRNA
Database
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PERFORMANCE TEST
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TARGET PREDICTION
Part of a parallel BBSRC tools and resources project
A high-throughput technique known as Parallel Analysis of
RNA Ends (PARE) is used to sequence mRNA cleavage
products on a large-scale
Sequence 5' end of uncapped mRNA (Degradome)
Including transcripts targeted by sRNAs and subjected to
endonucleolytic cleavage
The sRNA and degradome data can be used to identify
interactions between sRNAs and their target mRNA
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PARESnip
PAREsnip can be used to search for genome-wide
interactions between all sRNAs and transcripts as well as
predicting targets of small groups of miRNAs
PAREsnip outputs all potential sRNA target duplexes
evidenced through the degradome
Features:
Categorisation system
Addo-Quaye et. al (2009)
Data structures based on m-way search trees and multithreaded optimisation
~90 mins to process 100k sequences of A. thaliana data
At least as sensitive to detecting targets as other tools
designed for this type of analysis or better
Folkes et. al. (2012) NAR
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PARESnip
Each coloured
rectangle represents
an interaction
The taller the
rectangle, the higher
the abundance
Tool tips provide
additional information
T-plots can also be
generated
Target information is given
on the right
Navigation controls allow
the user to simply click
through the plots or output
them to PDF for publication
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OTHER TOOLS
miRProf (micro RNA Profiler)
Detect all known miRNAs found in miRBase within your
dataset
Griffiths-Jones, (2010)
Determines normalised expression levels of known miRNA
found in miRBase
Can be used to compare expression levels across multiple
samples
TA-SI prediction (Trans Acting Small Interfering RNA prediction)
Predicts phased ta-siRNA in plant datasets
Chen et. al. (2007)
Requires sRNA database and genome database
View phased sRNAs as they appear on the genome
SiLoCo...
Multi sample general loci prediction
Expression profile
DEFAULT STYLES
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ONLINE AVAILABILITY
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srna-workbench.cmp.uea.ac.uk
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STATS
Since launch on 27th Jan 2011
Total Visitors: 3,925
Page Views: 14,650 (3.73 pages per visit)
•Average time on site: 4.27 mins
•Total Version 2 Downloads: 1,200
•Around 30 collated requests for the RSS feed per day
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STATS
•Visits from 57 countries/territories
UK top visitor then USA...
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PUBLICATIONS
Stocks, M. B.; Moxon, S.; Mapleson, D.; Woolfenden, H. C.;
Mohorianu, I.; Folkes, L.; Schwach, F.; Dalmay, T. & Moulton, V.
(2012) The UEA sRNA Workbench: A Suite of Tools for Analysing
and Visualising Next Generation Sequencing microRNA and Small
RNA Datasets. Bioinformatics
Folkes, L.; Moxon, Simon.; Woolfenden, H.C.; Stocks, M.B.; Szittya,
G.; Dalmay, T.: Moulton, V.; (2012) PAREsnip: a tool for rapid
genome-wide discovery of small RNA/target interactions
evidenced through degradome sequencing. Nucleic Acids
Research
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ACKNOWLEDGEMENTS
Vincent Moulton
Tamas Dalmay
Simon Moxon
Frank Schwach
Irina Mohorianu
Dan Mapleson
Hugh Woolfenden
Leighton Folkes
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ANY QUESTIONS?
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