The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. The functionality of this software module has been described in Rissman et al. 2009, a publication in Bioinformatics. The Mauve Contig Mover can ease a comparative study between draft and reference sequences by ordering draft contigs according to the reference genome. In many cases, true rearrangements in the draft relative to the reference can be identified. The quality of the reorder is limited by the distance between the sequences, as indicated by the amount of shared gene content among the two organisms. A more distant reference will usually yield fewer ordered draft genome contigs, and may also induce erroneous placements of draft contigs. In addition to ordering contigs, MCM also orient them in the most likely orientation, and, if annotated sequence features are specified in an input file (e.g. with GenBank format input for the draft), MCM will output adjusted coordinates ranges for the features.

Outputs:

"Backbone" is the backbone output by mauveAligner representing the alignements.

"Reordered" is a fasta file with the contigs reordered. Contigs aligned in reverse will be thier compliment sequence.

"Contig Order" acts as an index to the fasta as the contig orders and orientations change (even if the draft was originally input as a genbank, after the first alignment, it will be converted to a fasta with annotation information preserved in a file described below). The file is divided into 3 sections, each containing a list of contigs. The data for each contig includes its label (name), its location in the genome (numbered in pseudocoordinates from the first to last contig, and whether it is oriented the same as originally input, or was complemented.

The three sections are described below:

Contigs to reverse:

This section contains contigs whose order is reversed with respect to the previous iteration. Note that contigs in this section may be oriented the same as originally input, this can be determined from the forward orcomplement designation.

Ordered Contings:

This is a list of all the contigs in the order and orientation they appear in the fasta for the draft of this iteration of the reorder. Since these include all the contigs in the original input, those with no ordering information (no aligned region) will be clustered at the end. These will appear as contigs with no LCBs at the end of the draft genome.

Contigs with Conflicting Order information:

This is a list of contigs containing LCBs suggesting multiple possible locations. These may be of interest to verify positioning, or to look at points of potential rearrangement or misassembly.

If the draft was input as an annotated genbank file, a second file will appear called "Features". This file will contain a line for each annotation, information about its current orientation and location (which will change if the contig is inverted), coordinates from the previous iteration (indicating relative orientation), and whether it is reversed from the original input. It will also have a label field used to identify each feature. This will be gotten from the annotation, as checked in the following order: db_xref, label, gene, and locus_tag.