{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T12:52:45Z","timestamp":1742388765106,"version":"3.37.3"},"reference-count":14,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2022,1,6]],"date-time":"2022-01-06T00:00:00Z","timestamp":1641427200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,1,6]],"date-time":"2022-01-06T00:00:00Z","timestamp":1641427200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1F30HL146095-01A1","K23AI125720","R01HL146377","R01AI141900","U19AI110820"],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2022,12]]},"abstract":"Abstract<\/jats:title>\n Background<\/jats:title>\n RIFINs and STEVORs are variant surface antigens expressed by P. falciparum<\/jats:italic> that play roles in severe malaria pathogenesis and immune evasion.<\/jats:italic> These two highly diverse multigene families feature multiple paralogs, making their classification challenging using traditional bioinformatic methods.<\/jats:p>\n <\/jats:sec>\n Results<\/jats:title>\n 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<\/jats:italic>. 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.<\/jats:p>\n <\/jats:sec>\n Conclusions<\/jats:title>\n STRIDE will be beneficial to malaria research groups analyzing genome sequences and transcripts of clinical field isolates, providing insight into parasite biology and virulence.<\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/s12859-021-04515-8","type":"journal-article","created":{"date-parts":[[2022,1,6]],"date-time":"2022-01-06T09:03:03Z","timestamp":1641459783000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families"],"prefix":"10.1186","volume":"23","author":[{"given":"Albert E.","family":"Zhou","sequence":"first","affiliation":[]},{"given":"Zalak V.","family":"Shah","sequence":"additional","affiliation":[]},{"given":"Katie R.","family":"Bradwell","sequence":"additional","affiliation":[]},{"given":"James B.","family":"Munro","sequence":"additional","affiliation":[]},{"given":"Andrea A.","family":"Berry","sequence":"additional","affiliation":[]},{"given":"David","family":"Serre","sequence":"additional","affiliation":[]},{"given":"Shannon","family":"Takala-Harrison","sequence":"additional","affiliation":[]},{"given":"Timothy D.","family":"O\u2019Connor","sequence":"additional","affiliation":[]},{"given":"Joana C.","family":"Silva","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6045-3322","authenticated-orcid":false,"given":"Mark A.","family":"Travassos","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,1,6]]},"reference":[{"key":"4515_CR1","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1038\/nature01097","volume":"419","author":"MJ Gardner","year":"2002","unstructured":"Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, et al. 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