STRIDE: a command‑line HMM‑based identifier and sub‑classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families
AuthorZhou, Albert E.
Shah, Zalak V.
Bradwell, Katie R.
Munro, James B.
Berry, Andrea A.
O'Connor, Timothy D.
Silva, Joana C.
Travassos, Mark A.
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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.
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.
Rights/TermsAttribution-NonCommercial-NoDerivatives 4.0 International
Identifier to cite or link to this itemhttp://hdl.handle.net/10713/21043
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Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivatives 4.0 International