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Comparisons and alignments

Plots that compare two or more sequences without losing orientation: alignments column by column, domain architectures, dotplots, synteny ribbons and gene neighbourhoods.

How to choose

Your question Plot Build it with
Where do aligned sequences disagree, column by column? Multiple alignment MsaTrack, --msa
Which domains does each protein carry, and in what order? Domain architectures DomainTrack, --domains
What shape is the rearrangement between two sequences? Dotplot DotplotTrack, --dotplot
Where did each block of one sequence go in the other, in a band that stacks with the rest? Synteny ribbons SyntenyTrack, --synteny
What does one genome's locus have that another's lacks? Gene neighbourhoods LocusTrack, --loci with --links

The dotplot and the ribbons take the same alignment blocks, so the same PAF file can be drawn either way. For two trees over the same taxa, use a tanglegram.

Plots

  • A conservation logo above an alignment of twelve isolates over 120 columns, each row a quiet bar with only the bases that disagree with the first isolate painted

    Multiple alignment Rows over alignment columns with only the disagreements painted, against the consensus or a row you name.

  • Twenty-two columns of a KatG protein alignment across five strains, every residue shown and coloured by physicochemical class, with one gap

    Protein alignment Every residue shown and coloured by one of six physicochemical classes.

  • Node bubbles and host bars on a rectangular tree, ancestral-host donuts on a radial tree, and an alignment and four protein architectures of sensor, repeat and kinase domains with rows sorted by the tree beside them

    Domain architectures Domains, motifs or repeats as labelled intervals, one protein per row and one colour per label; a tree beside the rows makes a gain or a loss read by clade.

  • Two M. tuberculosis chromosomes compared as a dotplot, where an inversion runs as an anti-diagonal and a translocated block sits off the main diagonal, above the same alignment drawn as ribbons

    Dotplot Alignment blocks as diagonals on two axes: an inversion is an anti-diagonal, and a translocation is a diagonal that has slid sideways.

  • An inversion close up: two sequence bars joined by ribbons that cross where the alignment reverses, above a feature marking the inverted segment

    Synteny ribbons The same blocks as ribbons between two bars, compact enough to stack under coverage and genes; an inversion is a twist.

  • The ESX-1 locus in H37Rv, M. bovis and BCG, genes drawn as arrows and joined by identity ribbons, with the block deleted in BCG left without ribbons

    Gene neighbourhoods One row per genome, genes as arrows and identity ribbons to the row below; genes with no match are outlined, because the absence is usually the finding.