START2 - Define your MLST scheme
Before you can load a MLST dataset, you must define the MLST scheme. The scheme definition describes the loci used and the location of allele and profile files. There is no limit to the number of schemes that can be defined.
- Bring up the scheme definition dialog by going to Define → MLST scheme.
- Enter the species name and click the 'Add scheme' button.
- Now, enter the names of each of the loci.
- The locus names will appear in a list box. The order of the loci can be changed by clicking the up and down arrows, or deleted by clicking the 'delete locus' button.
- For each of the loci, you can also enter the following information.
- ORF - open reading frame: select from all six reading frames or leave undefined. Analyses that require the ORF to be known will attempt to autodetect it and then auto-enter it if you leave it undefined.
- Standard length: all sequences loaded for a locus must be of a standard length (this can include gaps, but the sequences must be aligned). If you leave this blank, it will be auto-entered the first time you load sequences for this locus.
- Sequence file location: the location of the FASTA file containing the known alleles for this locus. This location can be on a local drive or on a network resource (e.g. web or FTP site). For MLST schemes hosted on pubmlst.org, allele sequences are available for download from http://pubmlst.org/data/.
- You can also enter the file location for the known allelic profiles. Again, this can be on a local drive or on a network resource. For MLST schemes hosted on pubmlst.org, profile files are available for download from http://pubmlst.org/data/.
- If you wish, you can export the scheme definition to a XML file. This can be re-imported in the future. It is, however, not necessary to save the scheme as it will be remembered the next time the program is run.
