What it does
Given a genome file in FASTA or Genbank format, MLST will scan the file against PubMLST typing schemes.
Output
MLST will produce a tab-seperated output file which contains: - the filename - the closest PubMLST scheme name - the ST (sequence type) - the allele IDs
Example Output
genomes/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3)
Without auto-detection
If you choose to manually set the MLST scheme, it will print a fixed tabular output with a heading containing allele names specific to that scheme (adjustable with Include allele header). To view a list of schemes, use the MLST List tool.
FILE SCHEME ST abcZ adk aroE fumC gdh pdhC pgm NM003.fa neisseria 11 2 3 4 3 8 4 6
Missing data
MLST does not just look for exact matches to full length alleles. It attempts to tell you as much as possible about what it found using the notation below:
| Symbol | Meaning |
|---|---|
| n | Exact intact allele |
| ~n | Novel full length allele similar to n |
| n? | Partial match to known allele |
| n,m | Multiple alleles |
| - | Allele missing |
Setting Output novel alleles to true will produce an additional novel_alleles.fasta file containing the novel alleles.
Galaxy wrapper maintained by Simon Gladman.