STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families
Year: 2022
Type: article
Abstract: BACKGROUND: 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.
Source: BMC Bioinformatics
Institution: University of Maryland, Baltimore
Language: English
Topic: Malaria Research and Control
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $2,690
Awards: Malaria variant surface antigen expression and vulnerability to disease in Malian children with Hemoglobin C trait, Protein microarray antibody responses to P. falciparum in a human challenge model, Variant surface antigens in cerebral malaria pathogenesis, Genome-wide sieve analysis and immunological validation to identify targets of protective efficacy in field trials of a whole-organism malaria vaccine, A Genomics Based Investigation of the Determinants of Polymicrobial Infectious Disease Outcomes, The role of RIFINs and their interaction with blood type in vulnerability to severe malaria in Malian children, Host vulnerability and parasite genetics in the development of cerebral malaria
OpenAlex ID: W4205797579