Alignment & variants

Dot plot (sequence comparison)

Word-match dot plot between two sequences, on both strands, returned as diagonal RUNS rather than points. This is the view that shows what a single best alignment hides: internal repeats, tandem duplications, and inversions — an inversion appears as a run on the falling diagonal and as nothing at all in a normal pairwise alignment. Compare a sequence with itself to map its own repeats. Word size is chosen from the input lengths when you do not set one, because too short a word fills the plot with chance matches that the eye reads as homology.

post/dot_plot

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/dot_plot
  • Auth: none required

Request body

astring required

First sequence (raw or FASTA). Max 200,000 nt.

bstring required

Second sequence. Pass the same sequence as "a" to find its internal repeats. Max 200,000 nt.

wordSizeinteger

Exact-match word length. Omit to pick one from the sequence lengths.

bothStrandsboolean

Also search the reverse complement, which is what reveals inversions.

minRunLengthinteger

Drop runs shorter than this before returning. 0 = keep every run at least wordSize long.

maxRunsinteger

Most runs to return, longest first.

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.