Locus Query - Multiple
Enter your query sequences into the text box for each locus, as in the screenshot below.
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 - your query sequences will be checked for the correct length and presence of non-DNA characters.
if the alleles are already in the database, the allele numbers are returned, as in the following screenshot:
If all of your alleles are found in the database, the Sequence Type is looked up and, if your allelic profile matches an ST already submitted to the database, the ST is also returned (in the above example, ST1).
For each locus, if no allele in the MLST database exactly matches your query, the sequence similarity of the most similar allele is returned as in the following screenshot:
The percentage identity to the closest match in the database is returned (aroE allele 1 in the above example) and the variant sites are shown.compared to the closest allele.
You can view an alignment of your query sequence against the closest matching allele, with the variant positions highlighted, by clicking 'Click here 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 Multiple Locus Query, you will be alerted to the fact that the allele is the wrong length, and there is an option to compare your sequence to 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 entered in the database of non-standard length alleles.
In the next section we detail the Batch Locus Query which allows you to query multiple sequences for a particular locus at one time.