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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?