Genome Alignment and Synteny Visualization Protocols

ZimingZhao,UpdatedJuly7th,2011,www.prism.gatech.edu/~zzhao31/

MUMmer: Pairwise genome alignment

Weblink: http://mummer.sourceforge.net/
Input: fasta formatted genome sequences (can be incomplete genomic sequence - contigs)
Command lines:
mummer -mum -b -c sequence1.fasta sequence2.fasta >out.mum
mummerplot -postscript -p 2D_out out.mum

Output: 2D plot

MAUVE: Multiple alignment of conserved genomic sequence with rearrangements.

Weblink: http://gel.ahabs.wisc.edu/mauve/alignments.php
Input: fasta formatted genome sequences (can be incomplete genomic sequence - contigs)
Command lines:
mauveAligner --output=mauve.out --output-alignment=mauve.alignment
--permutation-matrix-out=mauve.permutation --backboneoutput=mauve.backbone seq1.fasta seq1.sml seq2.fasta seq2.sml
seq3.fasta seq3.sml

Output:
1. mauve.outandmauve.alignmentcanbeopenedasagraphicinterfaceandit
islinkedtoGRIMM,whichcangivethegenomephylogenybasedon
rearrangementevents;
2. mauve.alignmentcontainstheLocallyCollinearBlocks(LCBs),whichare
usedforSNPanalysis.