STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families.
Bioinformatics
Hidden Markov models
Malaria
Plasmodium falciparum
RIFIN
STEVOR
Journal
BMC bioinformatics
ISSN: 1471-2105
Titre abrégé: BMC Bioinformatics
Pays: England
ID NLM: 100965194
Informations de publication
Date de publication:
06 Jan 2022
06 Jan 2022
Historique:
received:
21
02
2021
accepted:
06
12
2021
entrez:
7
1
2022
pubmed:
8
1
2022
medline:
11
1
2022
Statut:
epublish
Résumé
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 (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. STRIDE will be beneficial to malaria research groups analyzing genome sequences and transcripts of clinical field isolates, providing insight into parasite biology and virulence.
Sections du résumé
BACKGROUND
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
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
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.
Identifiants
pubmed: 34991452
doi: 10.1186/s12859-021-04515-8
pii: 10.1186/s12859-021-04515-8
pmc: PMC8733436
doi:
Substances chimiques
Antigens, Protozoan
0
Antigens, Surface
0
Protozoan Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
15Subventions
Organisme : NIH HHS
ID : R01HL146377
Pays : United States
Organisme : NIH HHS
ID : K23AI125720
Pays : United States
Organisme : NIH HHS
ID : R01AI141900
Pays : United States
Organisme : NIAID NIH HHS
ID : U19 AI110820
Pays : United States
Organisme : NIH HHS
ID : U19AI110820
Pays : United States
Organisme : NHLBI NIH HHS
ID : F30 HL146095
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL146377
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI141900
Pays : United States
Organisme : NIH HHS
ID : 1F30HL146095-01A1
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL130750
Pays : United States
Informations de copyright
© 2021. The Author(s).
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