Alignment & variants

Pairwise Alignment

Global (Needleman-Wunsch), local (Smith-Waterman) or semi-global/fitting pairwise alignment of two sequences, with match/mismatch scoring and affine gap costs (Gotoh).

post/pairwise_alignment

Request

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

Request body

seqAstring required

First sequence (raw or FASTA; nucleotide or protein).

seqBstring required

Second sequence (raw or FASTA; nucleotide or protein).

mode'global' | 'local' | 'semiglobal'

"global" penalizes end gaps in both sequences; "local" returns the best-scoring subalignment; "semiglobal" is a fitting alignment — seqB is consumed end to end while seqA's terminal overhangs are free and are not emitted, so a partial read placed on a longer reference is not smeared across it.

matchnumber

Match score.

mismatchnumber

Mismatch penalty.

gapnumber

Affine gap EXTEND penalty, charged per gap position (including the first).

gapOpennumber

Extra one-off penalty charged on top of gap for a gap's first position. Defaults to 1.5 * gap, so a k-base gap costs gap * (k + 1.5) and one contiguous k-base indel is cheaper than k scattered 1-base gaps. Pass 0 for a purely linear penalty.

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.