Serratus (virology)

Virus Discovery Platform

Serratus

Stable release|

v210110 / January 10th 2023

Operating system| Linux, web-based
Type| Bioinformatics
License| code, GPLv3. data, cc0
Website| serratus.io

Serratus is a large scale viroinformatics platform for uncovering the total genetic diversity of Earth's virome. Originating with the goal of uncovering novel coronaviruses[1] that may have been incidentally sequenced by other researchers, the project expanded to encompass all RNA viruses, those which encode a viral RNA-dependent RNA polymerase (RdRp).

By the end of 2020 there were approximately 15,000 distinct RNA virus sequences known from public databases, measured by the number of distinct RdRp (greater than 10% difference in amino acid sequence). Using a bioinformatics workflow optimized for large-scale cloud computing, the research team analyzed 5.7 million freely available sequencing datasets (20.4 petabytes of raw data) in the Sequence Read Archive (SRA) in only 11 days and a computing cost of US$23,900.[2] This analysis yielded 132,000 novel viral RdRp, representing nearly an order of magnitude increase in the known genetic diversity of RNA viruses.[3]

Within the database, RNA viruses are classified according to their RdRp palmprint,[4] a type of molecular barcode. The palmprint can be used as a computationally efficient index for the identification of which SRA sequencing runs contain a particular RNA virus. Such an index allows for targeted analysis of raw sequencing datasets from which novel RNA viruses can be characterized.[5]

All Serratus data are freely-available under the INDSC release policy.

## References

[edit]

1. ^ Pennisi, Elizabeth. "New dangers? Computers uncover 100,000 novel viruses in old genetic data". www.science.org. Science. Retrieved 13 January 2023.
2. ^ Pelley, Lauren. "Supercomputer helps Canadian researcher uncover thousands of viruses that could cause human diseases". CBC. Retrieved 13 January 2023.
3. ^ Edgar RC, Taylor J, Lin V, Altman T, Barbera P, Meleshko D, et al. (2022). "Petabase-scale sequence alignment catalyses viral discovery". Nature. 602 (7895): 142–147\. Bibcode:2022Natur.602..142E. doi:10.1038/s41586-021-04332-2. PMID 35082445. S2CID 221141152.
4. ^ Babaian, Artem; Edgar, Robert (13 October 2022). "Ribovirus classification by a polymerase barcode sequence". PeerJ. 10: e14055. doi:10.7717/peerj.14055. ISSN 2167-8359. PMC 9573346. PMID 36258794.
5. ^ Cabrera Mederos, Dariel; Debat, Humberto; Torres, Carolina; Portal, Orelvis; Jaramillo Zapata, Margarita; Trucco, Verónica; Flores, Ceferino; Ortiz, Claudio; Badaracco, Alejandra; Acuña, Luis; Nome, Claudia; Quito-Avila, Diego; Bejerman, Nicolas; Castellanos Collazo, Onias; Sánchez-Rodríguez, Aminael; Giolitti, Fabián (October 2022). "An Unwanted Association: The Threat to Papaya Crops by a Novel Potexvirus in Northwest Argentina". Viruses. 14 (10): 2297. doi:10.3390/v14102297. ISSN 1999-4915. PMC 9610017. PMID 36298852.

## External links

[edit]

* Official website
* palmID: RdRp sequence search tool
* Serratus code repository

* v
* t
* e

Bioinformatics

Databases|

* Sequence databases: GenBank, European Nucleotide Archive, DNA Data Bank of Japan and China National GeneBank
* Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource
* Other databases: BioNumbers, Protein Data Bank, Ensembl, InterPro, KEGG, and Gene Ontology
* Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase, VectorBase, WormBase, Rat Genome Database, PHI-base, Arabidopsis Information Resource, GISAID and Zebrafish Information Network

Software|

* BLAST
* Bowtie
* Clustal
* EMBOSS
* HMMER
* MUSCLE
* PANGOLIN
* SAMtools
* SOAP suite
* TopHat

Other|

* Server: ExPASy
* Rosalind (education platform)

Institutions|

* Broad Institute
* Computational Biology Department (CBD)
* Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI)
* Database Center for Life Science (DBCLS)
* DNA Data Bank of Japan (DDBJ)
* European Bioinformatics Institute (EMBL-EBI)
* European Molecular Biology Laboratory (EMBL)
* Flatiron Institute
* J. Craig Venter Institute (JCVI)
* Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
* US National Center for Biotechnology Information (NCBI)
* Japanese Institute of Genetics
* Netherlands Bioinformatics Centre (NBIC)
* Philippine Genome Center (PGC)
* Scripps Research
* Swiss Institute of Bioinformatics (SIB)
* Wellcome Sanger Institute
* Whitehead Institute

Organizations|

* African Society for Bioinformatics and Computational Biology (ASBCB)
* Australia Bioinformatics Resource (EMBL-AR)
* European Molecular Biology network (EMBnet)
* International Nucleotide Sequence Database Collaboration (INSDC)
* International Society for Biocuration (ISB)
* International Society for Computational Biology (ISCB)
* Student Council (ISCB-SC)
* Institute of Genomics and Integrative Biology (CSIR-IGIB)
* Japanese Society for Bioinformatics (JSBi)

Meetings|

* Basel Computational Biology Conference‎ ([BC2])
* European Conference on Computational Biology (ECCB)
* Intelligent Systems for Molecular Biology (ISMB)
* International Conference on Bioinformatics (InCoB)
* International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB)
* ISCB Africa ASBCB Conference on Bioinformatics
* Pacific Symposium on Biocomputing (PSB)
* Research in Computational Molecular Biology (RECOMB)

File formats|

* CRAM format
* FASTA format
* FASTQ format
* NeXML format
* Nexus format
* Pileup format
* SAM format
* Stockholm format
* VCF format
* GFF format
* GTF format

Related topics|

* Computational biology
* List of biobanks
* List of biological databases
* Molecular phylogenetics
* Sequencing
* Sequence database
* Sequence alignment

* Category
* Commons

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