Genome Content Management: A Tale of Small RNA

Genome Content ManagementA Tale of Small RNA

William Spoonerwhs@eaglegenomics.com

@whsqwghlm

eSI workshop on data flows in NGS

Eagle: An Open Source Business

Consultancy/advice Training Support Installation/Integration Customization Out sourced management

BusinessOpen Community(e.g. Academia)

Service Company

ServiceCollaboration

The Sequencing Cliff

$1000 genome~$0.01 Mbase (30x coverage)

Bioinformatics Crash Landing?

What needs to change?

The following must increase:

1. Number/efficiency of bioinformaticians,

2. Hardware scalability,

3. Software quality.

Survey – Attitudes to OS Software

/relia

fficien

ercial

IrreleventUsefulImportant

Technical attributes win

Technical attributes: WIN

Usability attributes lose

Usability attributes: LOSE

Source - http://eaglegenomics.com/survey

BUT…CAN THIS APPROACH SCALE?

Bioinformaticians like to;

• Develop their own solutions,

• Using open-source software,

• That’s stable, reliable, and published.

Bioinformaticians don’t like to;

•Develop user-friendly, supported software,

•Or train others to use it.

Is this the Answer?

“Genome Content Management is the set of processes and technologies that support the creating, managing, and reporting of genomic data.”

Create

Report

Create

Report

Manage

TIMELINE: Bespoke….Common Models….Content Management Systems

Genome Content Management Systems (G-CMS)

base O

Open Source Proprietary

Ensembl as a GCMS

Comparative Genomics

Functional Genomics

Variation

Assembly/GenesData Integration

Data Reporting

Data Analysis

Data Integration

Data Querying

Data QC

Auto-Scaling Ensembl

Databases Activities

APIDatabases Activities

Databases Activities

ActivitiesActivities

miRNA Prediction

Addfurther metrics to each transcript, e.g.:

MiRDeep Friedländer et. al. 2008

MiPred Jiang et. al. 2007

Drosha Site Finder Helvik et. al. 2007

RNAFold/RNAeval Gruber et. Al. 2008

Align small RNA reads to genome, store expressed regions

Test regions for stable secondary structure, store transcripts

Ensembl eHivebased

miRNAPrediction

Small RNA-Seq

Example Prediction: G.ga Chr. 19gga-mir-142 CACAGTACACTCATCCATAAAGTAGGAAACACTACACCCTGCAGTGCTGTTTAGTAGTGCTTTCTACTTTATGGGTGACTGCACTGTCgga-miR-142-3p/gga-miR-142-5p CCATAAAGTAGGAAACACTACA GTAGTGCTTTCTACTTTATGGG

IAH_G0249505300 .((.((.((((((((((((((((((.((((((.....(((....)))...)))))).)))))))))))))))))).)).)) IAH_G0249505300 AGTACACTCATCCATAAAGTAGGAAACACTACACCCTGCAGTGCTGTTTAGTAGTGCTTTCTACTTTATGGGTGACTGCACKN-1523_BP25_NR000026458 AGTACACTCATCCATAAAGTAGGAAACACTAC.................................................KN-1523_BP25_NR000050389 .GTACACTCATCCATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000037148 ..TACACTCATCCATAAAGTAGGAAACACTAC.................................................KN-1523_BP25_NR000055284 .......TCATCCATAAAGTAGGAAACACT...................................................KN-1523_BP25_NR000055535 ........CATCCATAAAGTAGGAAACACTA..................................................KN-1523_BP25_NR000026404 ........CATCCATAAAGTAGGAAACACT...................................................KN-1523_BP25_NR000044105 ........CATCCATAAAGTAGGAAACACT...................................................KN-1523_BP25_NR000031787 ........CATCCATAAAGTAGGAAACACTAC.................................................KN-1523_BP25_NR000031957 .........ATCCATAAAGTAGGAAACACTAC.................................................KN-1523_BP25_NR000022166 .........ATCCATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000045530 .........ATCCATAAAGTAGGAAACACTA..................................................KN-1523_BP25_NR000046154 .........ATCCATAAAGTAGGAAACACTAC.................................................KN-1523_BP25_NR000037676 ..........TCCATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000032163 ..........TCCATAAAGTAGGAAACACTAC.................................................KN-1523_BP25_NR000065952 ..........TCCATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000064893 ..........TCCATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000060177 ..........TCCATAAAGTAGGAAACACTA..................................................KN-1523_BP25_NR000054812 ...........CCATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000058317 ...........CCATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000007107 ...........CCATAAAGTAGGAAACACTA..................................................KN-1523_BP25_NR000055367 ...........CCATAAAGTAGGAAACACTAC.................................................KN-1523_BP25_NR000016790 ...........CCATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000041436 ...........CCATAAAGTAGGAAACACTAC.................................................KN-1523_BP25_NR000034949 ...........CCATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000008209 ...........CCATAAAGTAGGAAACAC....................................................KN-1523_BP25_NR000060347 ...........CCATAAAGTAGGAAACACTAC.................................................KN-1523_BP25_NR000002912 ...........CCATAAAGTAGGAAACACTAC.................................................KN-1523_BP25_NR000006332 ...........CCATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000038759 ............CATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000049956 ............CATAAAGTAGGAAACACTAC.................................................KN-1523_BP25_NR000048198 .............ATAAAGTAGGAAACACTACA................................................KN-1523_BP25_NR000042788 ...............................................TTAGTAGTGCTTTCTACTTTAT............KN-1523_BP25_NR000051592 .................................................AGTAGTGCTTTCTACTTTATG...........KN-1523_BP25_NR000064475 .................................................AGTAGTGCTTTCTACTTTATG...........KN-1523_BP25_NR000065559 ..................................................GTAGTGCTTTCTACTTTATG...........KN-1523_BP25_NR000031530 ....................................................AGTGCTTTCTACTTTATG...........KN-1523_BP25_NR000049786 ....................................................AGTGCTTTCTACTTTATGGG.........KN-1523_BP25_NR000000111 .....................................................GTGCTTTCTACTTTATGGG.........

KnownmiRNA

PredictedmiRNA

Droshasite

Conclusions

• This talk;

• Started with a business model,

• Ended with a sequence annotation,

• The two are linked by content management;

• Reuse• Extend• Share

Acknowledgements

• Mick Watson

- Institute of Animal Health

• Nick James

- Eagle Genomics Ltd.

• Madhu Donepudi

- Eagle Genomics Ltd.

Bioinformatics in the age of the

$1000 Genome?

http://eaglegenomics.com/survey

Genome Content Management: A Tale of Small RNA

Technology

Comparative Study of Small RNA and Small Peptides in Complete Genome Sequences

The invasive MED/Q Bemisia tabaci genome: a tale of gene

Human Genome & Genome Browser · PDF fileHuman Genome & Genome Browser ... • Acts by either causing RNA degradation or inhibition ... recruitment of histone modifiers

SPECIFIC CLEAVAGE OF HEPATITIS C VIRUS RNA GENOME BY HUMAN RNase P

RNA genome conservation and secondary structure …...2020/03/27 · the RNA synthesis pathway.8 Beyond these canonical structured regions, the RNA structure of the SARS-CoV-2 genome

AGOUTI: improving genome assembly and annotation using ...Keywords: Genome assembly, Scaffolding, Genome annotation, RNA sequencing, RNA-seq Background Findings Genomes sequenced using

Phytophthora Small RNA Database: Visualization of Small RNAs Using a Genome Viewer

MedChem 401 RNA Viruses These viruses contain a genome composed of RNA Remember plus-sense vs. minus-sense RNA genomes Remember RNA-dependent RNA polymerases

SIRT1 inhibits EV71 genome replication and RNA translation ... · RESEARCH ARTICLE SIRT1 inhibits EV71 genome replication and RNA translation by interfering with the viral polymerase

Next-generation transcriptome assembly · transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq

A tale of genome, annotations, metabolism and ...A tale of genome, annotations, metabolism and phylogenomics: the pea aphid genome resources Fabrice Legeai1,2, Stefano Colella3,4,

HOW CELLS READ THE FROM DNA TO RNA GENOME: FROM THE …mcb.berkeley.edu/courses/mcb110/Albertsch06.pdf · HOW CELLS READ THE GENOME: FROM DNA TO PROTEIN 6 FROM DNA TO RNA FROM RNA

Genome-wide profiling of RNA editing sites in sheep

Genome Assembly and De Novo RNA- seq

2014 RNA structure analysis of alphacoronavirus terminal genome regions

2013 Long-Distance RNA-RNA Interactions in the Coronavirus Genome Form High-Order Structures Promoting Discontinuous RNA

Plant molecular genetics Plant genome Chromatine and DNA methylation RNA interference Genome of plastids and mitochondria Transposible elements Viruses

Genome Wide Searches for RNA Secondary Structure Motifs

RNA-Seq primer - Bioinformatics Corebioinfo.umassmed.edu/content/pdf2015fall/week_3.mg.pdf · Sequencing libraries to probe the genome • RNA-Seq – Transcriptional output – Annotation

Quantitative RNA Sequencing (RNA-seq) and Exome … 1 HMGP 7620: Advanced Genome Analysis Quantitative RNA Sequencing (RNA-seq) and Exome Analysis Richard A. Radcliffe, Ph.D. Professor