Abstract
BackgroundRIFINs 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.ResultsSTRIDE (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.ConclusionsSTRIDE will be beneficial to malaria research groups analyzing genome sequences and transcripts of clinical field isolates, providing insight into parasite biology and virulence.
Highlights
RIFINs and subtelomeric variable open reading frame (STEVOR) are variant surface antigens expressed by P. falciparum that play roles in severe malaria pathogenesis and immune evasion
The eukaryotic parasite Plasmodium falciparum features the repetitive interspersed family (RIFIN) and subtelomeric variable open reading frame (STEVOR) multigene family, variant surface antigens that are associated with severe malaria pathogenesis and immune evasion [1,2,3]
RIFINs and STEVORs share a domain architecture, RIFINs can be further subtyped into RIFIN-As and -Bs based on a 25 amino acid indel in the semi-conserved domain and differences in subcellular localization suggestive of distinct functions (Fig. 1) [4, 5]
Summary
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. 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. The eukaryotic parasite Plasmodium falciparum features the repetitive interspersed family (RIFIN) and subtelomeric variable open reading frame (STEVOR) multigene family, variant surface antigens that are associated with severe malaria pathogenesis and immune evasion [1,2,3]. While RSpred addressed these concerns, it was web-based, could only evaluate ten sequences per job, and its web interface is no longer responsive
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