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Instructions

Introduction

MLST-Maps
    eBURST
    Trees

Database Query
    Results
    Maps

    eBURST
    Trees
    Download Data

Locus Query
    Sinlgle

    Multiple
    Batch

ST & Profile Query
    Sinlgle
    Batch
    ST Query

eBURST
    User data
    Geographic

Downloading Data

Organism Specific

Submitting Data
    alleles
    Sequence Types
    Isolate data
    Next-gen data

 

Policy Document

Locus Query - Batch

The Batch Locus Query allows you to paste in a set of query sequences at a particular locus and obtain the allele numbers, where known.

 

Your sequence should be cut and pasted into the box in FASTA or MEGA format.

Check carefully that the appropriate MLST locus has been selected.

NOTE: For each locus, an example of the correctly trimmed sequence of a typical allele can be obtained by clicking 'Click here for example data'.

Click 'Click and Wait' to submit your query sequences. Each will be checked for the correct length and presence of any non-DNA characters.

 

if the allele is already in the database, the allele number is returned, as in the following screenshot showing output for a batch of three aroE sequences:

 

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For each query sequence, if no exact match is found in the MLST database, the % sequence similarity to the most similar allele is returned, along with the position(s) and nucleotide difference(s) of the site(s) that differ, as in the following screenshot:

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You can view an alignment of your query sequence against the closest matching allele, with the variant positions highlighted, by clicking 'Click to view alignment', as in the following screenshot:

 

Non-Standard Length alleles

In MLST there may be rare alleles at a locus that are not the nomal length, typically differing by the inserion or deletion of one or a few codons. If you enter a non-standard length allele within the batch locus query, you will be alerted to the fact that the allele is the wrong length, and there is an option to compare the sequence to that of any alleles of non-standard length that are already in the database, as in the screenshot below.

If you think your allele is of a non-standard length, and does not correspond to a known non-standard length allele, you should submit the sequence, and the trace files, to the curator and it will be checked, assigned an allele number, and will be entered in the database of non-standard length alleles.

assume in in colour as the option is not available!

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Next we detail the ST and Profile Query section of the MLST websites which allows you, once you have assigned the alleles at each locus for your isolate, to query the allelic profile to discover your ST.

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