01 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 02 PROJECT AIMS

03 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

05 ANALYSIS TOOLS

06 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....

07 miRCat threading sRNA 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 08

09 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

10 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 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

11 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

18 ONLINE AVAILABILITY

19 srna-workbench.cmp.uea.ac.uk

20 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

21 STATS Visits from 57 countries/territories UK top visitor then USA...

22 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

23 ACKNOWLEDGEMENTS Vincent Moulton Tamas Dalmay Simon Moxon Frank Schwach Irina Mohorianu Dan Mapleson Hugh Woolfenden Leighton Folkes

24 ANY QUESTIONS?