Tool to detect small inversion in plastome
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?
1 answer
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
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