Tool to detect small inversion in plastome

Question

[wes]

The complete plastome of tropical fruit Garcinia mangostana (Clusiaceae) reported that there is a 363 bp inversion between trnV-UAC and atpE gene.

May I know is there any tool can be used to detect small inversion within the plastome sequence as reported above?

Answer 1

[cmdcolin]

You can compare two sequences and look at it in a dotplot or synteny style view to visually see the result. To automatically detect inversions, may need a structural variant caller

See https://mummer.sourceforge.net/manual/AlignmentTypes.pdf for dotplot interpretation from mummer

[wes]

thanks for the suggestion. Will give it a try