Locus Query - Single
Your query sequence should be cut and pasted into the text box, as in the screenshot below.
Check carefully that the appropriate MLST locus has been selected and that the raw sequence has been trimmed correctly.
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 sequence will be checked for the correct length and for the absence of any non-DNA characters. If the sequence is the wrong length, or contains characters other that A,T,G or C (upper or lower case can be used), you will get an error message.
if the allele is already in the database, the allele number is returned, as in the following screenshot:
Once the data has been submitted, the 'DNA-Jalview' button can be used to open a new window that will allow the sequence of the query allele to be compared with those of all alleles in the MLST database you are using (click on the 'DNA-JalView' button in the above window). This is useful for checking potentially novel alleles - there may be alleles in the database that only differ from the query allele at a single nucleotide site. If so, it is recommended that you carefully check such sites, in case the nucleotides at these positions are ambiguous or unclear in your sequence.
Once you have carefully checked the DNA sequencer traces (forward and reverse reads), the novel allele sequence and the forward and reverse trace files should be submitted to the curator, so that it can be checked, entered in the MLST database, and an official allele number assigned.
If no allele in the MLST database exactly matches your query sequence, 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 (in this example, allele 1, and the positions that differ between the query sequence and that of the most similar allele are shown.
You can view an alignment of your query sequence against the closest matching allele sequence, 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 query with a non-standard length sequence, you will be alerted to the fact that the allele is the wrong length, and (after carefully checking your sequence trace files and the correct trimming) you should compare your non-standard length allele with any alleles of non-standard length that are already in the database, as shown in the screenshot below.
If you think your allele is of 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 a new allele number, and entered in the database of non-standard length alleles.
In the next section we describe the Multiple Locus Query which allows you to query the sequences from all MLST loci at one time.