ecoli_mlst

ecoli_mlst is a script to determine MLST sequence types for E. coli genomes and extract allele sequences.

• Synopsis
• Description
• Usage
• Options
  • Mandatory options
  • Optional options
• Output
• Run environment
• Author - contact
• Citation, installation, and license
• Changelog

Synopsis

perl ecoli_mlst.pl -a fas -g fasta

Description

The script searches for multilocus sequence type (MLST) alleles in E. coli genomes according to Mark Achtman's scheme with seven house-keeping genes (adk, fumC, gyrB, icd, mdh, purA, and recA) [Wirth et al., 2006]. NUCmer from the MUMmer package is used to compare the given allele sequences to bacterial genomes via nucleotide alignments.

Download the allele files (adk.fas ...) and the sequence type file ('publicSTs.txt') from this website: http://mlst.ucc.ie/mlst/dbs/Ecoli

To run ecoli_mlst.pl include all E. coli genome files (file extension e.g. 'fasta'), all allele sequence files (file extension 'fas') and 'publicSTs.txt' in the current working directory. The allele profiles are parsed from the created *.coord files and written to a result file, plus additional information from the file 'publicSTs.txt'. Also, the corresponding allele sequences (obtained from the allele input files) are concatenated for each E. coli genome into a result multi-fasta file. Option -c can be used to initiate an alignment for this multi-fasta file with ClustalW (standard alignment parameters; has to be in the $PATH or change variable $clustal_call). The alignment fasta output file can be used directly for RAxML. CAREFUL the Phylip alignment format from ClustalW allows only 10 characters per strain ID.

ecoli_mlst.pl works with complete and draft genomes. However, several genomes cannot be included in a single input file!

Obviously, only for those genomes whose allele sequences have been deposited in Achtman's allele database results can be obtained. If an allele is not found in a genome it is marked by a '?' in the result profile file and a place holder 'XXX' in the result fasta file. For these cases a manual NUCmer or BLASTN might be useful to fill the gaps and run_sub_seq.pl to get the corresponding 'new' allele sequences.

Non-NCBI fasta headers for the genome files have to have a unique ID directly following the '>' (e.g. 'Sakai', '55989' ...).

Usage

perl ecoli_mlst.pl -a fas -g fasta -c

Options

Mandatory options

• -a, -alleles

  File extension of the MLST allele fasta files, e.g. 'fas' (<=> -g).

• -g, -genomes

  File extension of the E. coli genome fasta files, e.g. 'fasta' (<=> -a).

Optional options

• -h, -help

  Help (perldoc POD)

• -c, -clustalw

  Call ClustalW for alignment

Output

• ecoli_mlst_profile.txt

  Tab-separated allele profiles for the E. coli genomes, plus additional info from 'publicSTs.txt'

• ecoli_mlst_seq.fasta

  Multi-fasta file of all concatenated allele sequences for each genome

• *.coord

  Text files that contain the coordinates of the NUCmer hits for each genome and allele

• (errors.txt)

  Error file, summarizing number of not found alleles or unclear NUCmer hits

• (ecoli_mlst_seq_aln.fasta)

  Optional, ClustalW alignment in Phylip format

• (ecoli_mlst_seq_aln.dnd)

  Optional, ClustalW alignment guide tree

Run environment

The Perl script runs only under UNIX flavors.

Author - contact

Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)

Citation, installation, and license

For citation, installation, and license information please see the repository main README.md.

Changelog

• v0.3 (30.01.2013)
  • additional info in POD
  • check if result files already exist and ask user what to do
  • changed script name from ecoli_mlst_alleles.pl to ecoli_mlst.pl
• v0.2 (20.10.2012)
  • included a POD
  • options with Getopt::Long
  • don't consider input E. coli genome query files, which are too big (set cutoff at 9 MB for a fasta E. coli file)
  • draft E. coli genomes can now be used as input query files
  • additional info in 'publicSTs.txt' now associated to found ST types in output
  • give text to STDOUT which files were created
  • new option -c to align the resulting allele sequences via ClustalW
• v0.1 (25.10.2011)