MLST pipeline

MLST specifications

Information


Unique identifier OMICS_12861
Name MLST
Alternative name MultiLocus Sequence Typing
Interface Web user interface
Restrictions to use None
Input data The method uses short sequence reads from sequencing platforms or preassembled genomes.
Input format FASTA, FASTAQ
Computer skills Basic
Version 1.8
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Mette V. Larsen <>

Publication for MultiLocus Sequence Typing

MLST IN pipelines

 (35)
2018
PMCID: 5794934
PMID: 29437087
DOI: 10.1128/genomeA.01223-17

[…] all parameters (9). contigs were organized by aligning to the genome sequence of the reference strain s. typhimurium lt2 (accession no. nc_003197) using mauve multiple alignments (10). whole-genome multilocus sequence typing was performed using enterobase (https://enterobase.warwick.ac.uk/). a total of three sequence types, st19 (n = 9), st1695 (n = 1), and st313 (n = 1), were identified. […]

2018
PMCID: 5845691
PMID: 29559964
DOI: 10.3389/fmicb.2018.00383

[…] the phylogenetic tree root was confirmed to be positioned between the two genomovar iiia and iiib by reiterating the same protocol with 29 additional burkholderia spp. genomes (data not shown)., multilocus sequence typing (mlst) of the seven studied strains was performed using seven standard housekeeping genes (atpd, gltb, gyrb, lepa, phac, trpb, and reca) according to the protocol […]

2018
PMCID: 5857380
PMID: 29345222
DOI: 10.1099/mgen.0.000153

[…] of new strains. there is, however, little information on the genetic diversity of the species, or on the relationship between strains. this is resolved in this study through the development of an multilocus sequence typing system. to facilitate use by the research community, a web-based database and tool was implemented to allow any researchers to easily type and classify more k. marxianus […]

2018
PMCID: 5897799
PMID: 29650569
DOI: 10.1128/genomeA.00223-18

[…] aarhus, denmark). the genomes were annotated using the rapid annotations using subsystems technology (rast) annotation server (13), and 16 sequence types were determined by using the cronobacter multilocus sequence typing (mlst) website (http://pubmlst.org/cronobacter). the genome sizes and coding sequences (cdss) of these assemblies ranged from 4.3 to 4.5 mb and 3,977 to 4,256, […]

2018
PMCID: 5897803
PMID: 29650582
DOI: 10.1128/genomeA.00290-18

[…] (24). automated annotation of the assembled contigs was performed using the ncbi prokaryotic genome annotation pipeline (https://www.ncbi.nlm.nih.gov/genome/annotation_prok/). whole-genome multilocus sequence typing was performed using the staphylococcus pseudintermedius mlst database (https://pubmlst.org/spseudintermedius/), as described previously (25). all of these strains displayed […]

MLST institution(s)
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; National Food Institute, Technical University of Denmark, Lyngby, Denmark; Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
MLST funding source(s)
Grant 09-067103/DSF, Danish Council for Strategic Research

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