0 1 The sRNA Workbench project date 20/07/2012 Matthew. B. Stocks
Jan 15, 2016
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The sRNA Workbench
project date 20/07/2012
Matthew. B. Stocks
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)
• Cross platform support
• To allow multiple analysis techniques from within a single program through the use of an MDI (Multiple Document Interface)
• Performance improvements, Speed, Memory
• Still accessible through the command line
Code maintainability
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PROJECT AIMS
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WHAT WE ALREADY OFFER
Adapter Removal
Removes 3’ and/or 5’ adaptors from raw high-throughput 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 04
HELPER TOOLS
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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 sRNA
CPU Core
CPU Core
sRNA Database
Thread Pool:FIFO data structure (Queue)
First sequence added to the list (First In) is the first item processed (First Out)
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 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 systemAddo-Quaye et. al (2009)Data structures based on m-way search trees and multi-
threaded 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
PARESnip
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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
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 12
OTHER TOOLS
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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 2011Total 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 MoultonTamas DalmaySimon MoxonFrank SchwachIrina Mohorianu Dan MaplesonHugh WoolfendenLeighton Folkes
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ANY QUESTIONS?