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dc.contributor.authorZhou, Albert E.
dc.contributor.authorShah, Zalak V.
dc.contributor.authorBradwell, Katie R.
dc.contributor.authorMunro, James B.
dc.contributor.authorBerry, Andrea A.
dc.contributor.authorSerre, David
dc.contributor.authorTakala‑Harrison, Shannon
dc.contributor.authorO'Connor, Timothy D.
dc.contributor.authorSilva, Joana C.
dc.contributor.authorTravassos, Mark A.
dc.descriptionThe article processing charges (APC) for this open access article were partially funded by the Health Sciences and Human Services Library's Open Access Publishing Fund for Early-Career Researchers.en_US
dc.description.abstractBackground: RIFINs and STEVORs are variant surface antigens expressed by P. falciparum that play roles in severe malaria pathogenesis and immune evasion. These two highly diverse multigene families feature multiple paralogs, making their classification challenging using traditional bioinformatic methods. Results: STRIDE (STevor and RIfin iDEntifier) is an HMM-based, command-line program that automates the identification and classification of RIFIN and STEVOR protein sequences in the malaria parasite Plasmodium falciparum. STRIDE is more sensitive in detecting RIFINs and STEVORs than available PFAM and TIGRFAM tools and reports RIFIN subtypes and the number of sequences with a FHEYDER amino acid motif, which has been associated with severe malaria pathogenesis. Conclusions: STRIDE will be beneficial to malaria research groups analyzing genome sequences and transcripts of clinical field isolates, providing insight into parasite biology and virulence.en_US
dc.relation.ispartofBMC Bioinformaticsen_US
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 International*
dc.subject.lcshHidden Markov modelsen_US
dc.subject.meshMalaria, Falciparumen_US
dc.subject.meshAntigens, Surfaceen_US
dc.subject.meshComputational Biologyen_US
dc.titleSTRIDE: a command‑line HMM‑based identifier and sub‑classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen familiesen_US

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Attribution-NonCommercial-NoDerivatives 4.0 International
Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivatives 4.0 International