Dimitris Karapliafis (@dkarap.bsky.social)

Dimitris Karapliafis

@dkarap.bsky.social

Dimitris Karapliafis reposted

@rdrpsummit.bsky.social

#RNAVirusJournalClub! The co-founder of RdRp Summit @urineri.bsky.social will introduce the #RolyPoly - a python library for various common virus analysis tasks. 🍁Thur, October 8th, 8am London time. 🍁 Hosted by the RdRp Summit 2027 lead: @marcoforgia.bsky.social 🍁 All welcome! 😊 #RdRpSummit

Dimitris Karapliafis

@dkarap.bsky.social

10 July

Very excited to share our paper (and first for my PhD) on RdRpCATCH in NAR Genomics and Bioinformatics! doi.org/10.1093/narg... Co-authors: @urineri.bsky.social, @ingrida.bsky.social, Justine Charon, @sho1.bsky.social, @xinhou.bsky.social, Dick de Ridder, Mark P. Zwart, and @annecmg.bsky.social

doi.orgRdRpCATCH: a unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov modelsAbstract. Recent advances in large-scale sequence mining have expanded our knowledge of RNA virus diversity. Most genome mining approaches for detecting RN

RdRpCATCH emerged as a community project from the first RdRpSummit @rdrpsummit.bsky.social; discussions with the database developers there inspired a unified, user-friendly workflow. We are very grateful for the support and for this project now being out there to support RNA virus discovery efforts!

Dimitris Karapliafis

@dkarap.bsky.social

10 July

Huge thanks to all co-authors and my PhD supervisors for entrusting me with this project and for their support. RdRpCATCH: – Web app: rdrpcatch.bioinformatics.nl – Code: github.com/dimitris-kar... #RNAvirus #metagenomics #bioinformatics #computationalvirology #RdRp #Viromics

rdrpcatch.bioinformatics.nlRdRpCATCH - Home

RNA viruses are incredibly diverse, and conventional similarity-based methods often fail to capture this diversity in sequencing datasets. Recent studies rely on detecting the marker RNA-dependent RNA polymerase (RdRp) using more sensitive approaches, such as profile Hidden Markov Models (pHMMs).

Dimitris Karapliafis

@dkarap.bsky.social

10 July

With RdRpCATCH, we compare all publicly available RdRp pHMM resources on curated datasets and bring them into one framework that: – Scans (meta)transcriptomic assemblies for RdRp signals – Flags putative RNA virus contigs – Provides provisional taxonomic annotation

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