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Blastocystis Subtype (18S) and Sequence Typing (MLST) Databases

This site uses two linked databases powered by the BIGSdb genomics platform. The sequence definition database contains allele sequence and MLST profile definitions whereas the isolate database contains provenance and epidemiological information. Further details about BIGSdb can be found in Jolley & Maiden 2010, BMC Bioinformatics 11:595.

In terms of genetic markers, the barcode region (Scicluna et al., 2006) is by far the best represented in publicly available sequence databases, and the correct subtype can be identified by BLAST analysis in the sequence database at the present site. Blasting against this database has the added advantages, compared to using GenBank, of automatically assigning allele types to the SSU-rDNA as well as using the consensus subtype nomenclature (unlike GenBank where the subtype is included only if one was part of the accession submission and no attempt to impose a standard nomenclature is made). In case the sequence does not match any of the ones in the database despite full coverage of the region, this indicates that the sequence represents a new allele or maybe even a new subtype depending on the amount of variation. If a new subtype is suspected, we suggest doing PCR and sequencing of the complete SSU rRNA gene with subsequent phylogenetic analysis using reference sequences.

ST3 and ST4 MLST schemes were developed by Rune Stensvold. The 18S typing scheme was developed by Aldert Bart.

Database curated by Rune Stensvold (MLST) Aldert Bart (18S).

Citing the database

The preferred format for citing this website in publications is:

This publication made use of the Blastocystis Sequence Typing website (https://pubmlst.org/ blastocystis/) developed by Keith Jolley and sited at the University of Oxford (Jolley & Maiden 2010, BMC Bioinformatics, 11:595). The development of this site has been funded by the Wellcome Trust.

Status

Sequence database
Sequences: 281
Profiles:
ST3 MLST: 60
ST4 MLST: 6

Isolate database
Isolates: 692
Last updated: 2012-02-16