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2. An Introductory Webinar Wojtek Bazant & Faye Rodgers

3. Outline Why WormBase ParaSite? Our genomes Data available BioMart
Questions

4. Why WormBase ParaSite?
Helminths (parasitic roundworms and flatworms) are the causative agents of many diseases of humans, animals and plants
Increasing amounts of genomic data are becoming available to the helminth research community
WormBase ParaSite processes and presents that data in a consistent and accessible way

5. Analyses run for all genomes
Genomes and primary annotation
(from the community)
Analyses run for all genomes
Protein domain prediction, GO term annotation, repeat annotation, ncRNA annotation, alignment of publicly available RNASeq data, linking IDs to external databases
Comparative analysis
Build gene trees incorporating all genomes in the release (plus comparators) to predict orthologues and paralogues.
Mention that
Website - browsing
Gene and species pages
JBrowse
Website - tools
BLAST
BioMart
REST API

6. Structure and features of the front page

7. Our genomes

8. Genome and species descriptions

9. Finding information related to your scientific question
If you know the gene name or ID, it’s just a search task! Otherwise, it more like research.
Common avenues:
BLAST the sequence
Text search to try match a gene description
Search through a protein feature or GO term
Navigate through an orthologous gene in other species
home page with some red circles

10. Data available for each gene

11. Transcript and protein pages

12. Data available for each gene

13. “Region in detail” - embedded genome browser

14. Alternative genome browser – JBrowse
Better for a workbench view with multiple tracks

15. Data available for each gene

16. Links and references - UniProt etc.

17. Literature

18. Comparative Genomics
Gene trees are computed with every release, classifying genes into families. These are reconciled with the species trees to infer orthologous and paralogous relationships.
Speciation node
Duplication node
Tree views can be configured for exploring the gene family

19. Comparative Genomics
Eg, highlight all of the paralogues:

20. Comparative Genomics
Orthologues and paralogues are also available in tabular format:
Lists can be exported from BioMart
Full gene trees can be accessed programmatically via the API

21. BioMart
A very powerful tool for accessing data in bulk without any programming knowledge.
Filters
The data type you’re basing your query on, eg:
Genome
Genomic region
A list of gene IDs
All genes annotated with a protein domain or a GO term
All genes that have an orthologue in a species
Values
The actual data you’re basing your query on, eg:
Schistosoma mansoni PRJEA36577
Schistosoma mansoni Sm_V7_1
Smp_035270, Smp_010250, Smp_244010…
SignalP
Genes with an orthologue in Schistosoma haematobium
Attributes
The data you want, eg:
Protein stable IDs
cDNA sequences
Uniprot IDs
Protein domains
Orthologue names, % identity
Filters can be combined to build more complex queries

22. BioMart
Walk-through example: using BioMart to retrieve S. mansoni genes from the ZW chromosome that have an orthologue in S. japonicum and S. haematobium. Want to return the S. mansoni, S. haematobium and S. japonicum gene IDs.

23. To access BioMart from the home page

24. Add a species filter

25. Add a region filter

26. Add homology filters

27. Count how many genes fulfil our filter criteria

28. Select output attributes

29. Previewing the results we get by default

30. Add orthologues to output attributes

31. Scroll down to find the species that we’re interested in

32. View a preview of your output, and download full results.

33. BioMart Other examples of questions that can be answered with BioMart:
For a list of gene IDs:
Convert to other types of identifier (Uniprot, RefSeq, NCBI)
Retrieve associated protein domains, GO terms
Retrieve their genomic coordinates
Generate FASTA files of protein, cDNA, UTR, flanking region sequences etc
Retrieve a list of genes that:
Have a given protein domain/GO term
Have/do not have orthologues in species X,Y,Z.
Are on genomic region X
For R users, WormBase ParaSite BioMart supports the biomaRt R package: see our help and documentation pages to get started.

34. Outline Why WormBase ParaSite? Our genomes Data available BioMart
Questions

35. If we don’t get to your question: email parasite-help@sanger.ac.uk
Outline
Why WormBase ParaSite?
Our genomes
Data available
BioMart
Questions
If we don’t get to your question:

36. Sample question The suggested option Other, more creative approaches?
I need the sequences for a set of Schistosoma mansoni genes. I have the chromosome, start, and stop for each.
The suggested option
Other, more creative approaches?
download the GFF and the sequence files from the FTP, and write a program
check the cases one by one
use the API, first „region” endpoint to get gene IDs, then „sequence” endpoint
the helpdesk ( it might work )

37. BioMart Example 2
Using BioMart to generate a protein FASTA file from a list of gene IDs

38. Select filter(s).

39. Paste in gene IDs.

40. In output attributes, select “Retrieve sequence”

41. Select the type of sequence we’re interested in.
Select the information we’d like in the FASTA header.

42. Preview and download output.

43. Upcoming webinars Don’t forget!
See the full list of upcoming webinars at
Don’t forget!
Please fill in the survey that launches after the webinar – thanks!