1. A web-based platform for structural and functional annotation of model and non-model organisms
Jodi Humann, Taein Lee, Stephen Ficklin, Chun-Huai Cheng, Heidi Hough, Sook Jung, Jill Wegrzyn, David Neale, Dorrie Main

2. What is genome annotation?
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Annotation
Predicted gene models to use in lab experiments

3. What is GenSAS? Web-based platform, no software installation by user
Just need a user account, internet browser, and an internet connection
User accounts keep data private and secure and allow for collaborative annotation projects
Easy-to-use interfaces and detailed user manual

4. Account Limits
User accounts will remain active as long there is an active project
Projects expire after 60 days unless user resets expiration date
250 GB of storage space on server
Assembly files must be high quality
<25,000 sequences
Over 50% of sequences longer than 2,500 bases
Seven jobs running at one time, but other jobs can be waiting in queue

5. Eukaryote annotation workflow
Upload Sequences
PRINSEQ-lite, BUSCO
Create Project
Upload Evidence
Identify Repeats
RepeatMasker, RepeatModeler
Mask Sequences
Align Evidence
BLAST, BLAT, DIAMOND, HISAT2, PASA, TopHat
Structural Annotation
Augustus, BRAKER2, GeneMarkES, Genscan, GlimmerM, SNAP, RNammer, tRNAScan-SE
Choose Official Gene Set
EvidenceModeler (optional)
Refine Gene Models
PASA (optional)
Functional Annotation
BLAST, DIAMOND, InterProScan, Pfam, SignalP, TargetP
Manual Curation
Apollo, JBrowse
Generate Files for Publication
BUSCO

6. Prokaryote annotation workflow
Upload Sequences
PRINSEQ-lite, BUSCO
Create Project
Upload Evidence
Align Evidence
BLAST, BLAT, DIAMOND
Structural Annotation
GeneMarkS, Glimmer3, RNAmmer, tRNAScan-SE
Choose Official Gene Set
Functional Annotation
BLAST, DIAMOND, InterProScan, Pfam, SignalP
Manual Curation
Apollo, JBrowse
Generate Files for Publication
BUSCO

7. User provided files Required: Optional: Genome assembly
Assembled transcripts or ESTs
Species-specific repeats or proteins
Species-specifc Genbank gene structures
Filtered Illumina RNA-seq reads
Aligned RNA-seq reads in the BAM file format
Previous annotations in the GFF3 format

8. GenSAS provided information
RepeatMasker:
Repbase repeat libraries
Transcript and protein alignment tools:
NCBI RefSeq transcripts and proteins
archaea, bacteria, fungi, invertebrate, mitochondrion, plant, plasmid, plastid, protozoa, vertebrate-mammalian, vertebrate- other, viral
SwissProt
Trembl

9. GenSAS Homepage Request free account Login to GenSAS
Access User’s Guide and contact us
Learn about tools and libraries
Access the GenSAS interface

10. Once jobs are in queue, users can log out of GenSAS
GenSAS Interface
Once jobs are in queue, users can log out of GenSAS

11. Sequences Step
Once uploaded, assembly metrics are calculated using PRINSEQ
Users can run BUSCO on assembly

12. Project Step Fillable web form Select previously uploaded assembly
options

13. GFF3 Step

14. Evidence Step

15. Repeats and Masking Steps
Masking step produces consensus, or can skip masking

16. Align Step

17. Structural Step

18. Consensus Step Optional step using EVM Can adjust and remove weights
Gene Predictions
Protein Alignments
Transcript Alignments

19. OGS Step
Select
“Official Gene Set”

20. Refine and Functional Steps
Optional step to further refine OGS using PASA prior to functional annotation

21. Annotate Step
Edits added to “User-created Annotations” will be merged into final results

22. Publish Step OGS and repeat consensus automatically prepared
FASTA and GFF formats
User can select other jobs

23. Final Annotation Results
Summary table of annotation project
Project Summary file with details about tool settings
Option to create merged GFF3 file
Add repeats, tRNA, rRNA
Add functional job annotation to column 9

24. Final Annotation Results
All results files are listed and can be downloaded individually or….

25. Final Annotation Results
Use “Download all” option to get all the files at once
Option to run BUSCO on proteins from final annotation

26. Funding
GenSAS Poster – PO0085