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Fig. 2 | BMC Bioinformatics

Fig. 2

From: STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families

Fig. 2

Stacked bar graphs of the sequence distribution from all available P. falciparum genomes from PlasmoDB v45 at the conclusion of training each HMM profile. A total of 3536 RIFIN and STEVOR sequences were downloaded from PlasmoDB (Release 45; August 28, 2019). Redundant sequences were clustered with CD-HIT v4.6. HMM (Hidden Markov Model) profiles specific for RIFIN-A, RIFIN-B, and STEVOR proteins were created and iteratively trained against subsets of sequences that were not present in the initial seeding. 967 RIFIN-A, 495 RIFIN-B, and 229 STEVOR sequences comprised the final datasets, providing representation of sequences from all genomes. The Malian (ML01) and Togo (TG01) strains were polyclonal and had overall higher numbers of representative sequences. Of the total of 228 RIFINs and STEVORs annotated in the 3D7 reference genome, STRIDE used 122 3D7 sequences

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BMC Bioinformatics

ISSN: 1471-2105

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