Querying allele sequences

There are four ways of querying allele sequences:

Single locus query

This is the method used by most people. Here you have a text box that a sequence can be pasted in to, and a drop-down list of loci. Simply paste your trimmed sequence into the text box, select the appropriate locus and press 'submit'. If the sequence is in the database, the allele number is returned. If the sequence is not in the database, you are told to which allele it is most similar and given a list of nucleotide positions where there are differences. There is also a link to display these two sequences aligned.

After you have queried the database, a button labelled 'sequence analysis' will appear at the bottom of the page. Pressing this will take you to a page from where you can start the Jalview alignment editor to display your query sequence against all know alleles, with polymorphisms highlighted.

Multiple locus query

This page contains a text box for each locus. Simply paste your sequences into the appropriate box and press 'submit'. You don't need to enter data in every box. If your allele sequences are known, the set of allele numbers are returned, if not, the identity of the nearest allele and the nucleotide positions of any differences are shown. If the allelic profile is complete the ST number is returned if found in the database.

Single locus batch query

This is a method that allows you to query a batch of sequences presented in MEGA or FASTA format. This is particularly useful for integrating the website/databases with automated tools such as STARS. The output is a text page, with one line per sequence, that can be parsed easily by computer. If a sequence is not matched, the most similar sequence is identified with a list of nucleotide differences.

BLAST

This method allows you to perform a BLAST search against all the MLST loci. This can be useful if you can't find the start or end of your locus, or if you think that your sequencing results have been mixed up! If your sequence is an identical match, it will tell you, otherwise you'll get a list of nearest matches. You can also click on the hyperlink to see the output from the BLAST algorithm.