L. anisa cgMLST 3140 targets ref-seqs.fasta

cgMLST scheme was constructed using the genomes of three L. anisa strains downloaded from NCBI (RefSeq:
NZ_CANP00000000.1; RefSeq: NZ_NBTX00000000.1; RefSeq: NZ_LNXS00000000.1), using
Ridom SeqSphere+ cgMLST Target Definer with the following parameters: a minimum
length filter that removes all genes smaller than 50 bp; a start codon filter
that discards all genes that contain no start codon at the beginning of the
gene; a stop codon filter that discards all genes that contain no stop codon or
more than one stop codon or that do not have the stop codon at the end of the gene;
a homologous gene filter that discards all genes with fragments that occur in
multiple copies within a genome (with identity of 90% and >100 bp overlap);
and a gene overlap filter that discards the shorter gene from the cgMLST scheme
if the two genes affected overlap >4 bp. The remaining genes were then used
in a pairwise comparison using BLAST version 2.2.12 (parameters used were word
size 11, mismatch penalty −1, match reward 1, gap open costs 5, and gap
extension costs 2). All genes of the reference genome that were common in all
query genomes with a sequence identity of ≥90% and 100% overlap and, with the
default parameter stop codon percentage filter turned on, formed the final
cgMLST scheme