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Multilocus sequence typing

This application is for taking MLST sources from multiple locations and consolidating them in one place so that they can be easily used (and kept up to date). Then you can provide FASTA files and get out sequence types for a given MLST database. Two spreadsheets are outputted, one contains the allele number for each locus, and the ST (or nearest ST), the other contains the genomic sequence for each allele.
If more than 1 allele gives 100% identity for a locus, the contaminated flag is set. Optionally you can output a concatenated sequence in FASTA format, which you can then use with tree building programs. New, unseen alleles are saved in FASTA format, with 1 per file, for submission to back to MLST databases.

It requires NCBI Blast+ to be installed and for blastn and makeblastdb to be in your PATH.

For any queries, contact path-help@sanger.ac.uk

Example usage

Add this environment variable to your ~/.bashrc file - do this once

export MLST_DATABASES=/path/to/where_you_want_to_store_the_databases

Download the latest copy of the databases (run it once per month)

download_mlst_databases

Find the sequence types for all fasta files in your current directory

get_sequence_type -s "Clostridium difficile" *.fa

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