GRAAu is an audit tool for genome rearrangement algorithms. The audit consists of comparing, for each permutation in the symmetric group, the distance outputted by a given rearrangement algorithm with the related rearrangement distance, which is obtained from the Rearrangement Distance Database, and producing statistics that can be used to analyze the performance of this algorithm.

Statistics

• Diameter: Greatest distance outputted by the rearrangement algorithm.
• Average Distance: Average of the distances outputted by the rearrangement algorithm.
• Average Ratio: Average of the ratios between the distance outputted by the rearrangement algorithm and the related rearrangement distance.
• Maximum Ratio: Greatest ratio among all the ratios between the distance outputted by the rearrangement algorithm and the related rearrangement distance.
• Equals: Percentage of distances outputted by the rearrangement algorithm that equals the related rearrangement distance.

In addition to the statistics, GRAAu outputs up to 50 permutations which exhibited the maximum ratio.

Downloads

File	Version	Description
graau.zip	1.00	GRAAu package.
graau_manual.pdf	1.00	GRAAu user's manual.

Ticket Generation

To generate a valid ticket, click here.

Rearrangement Model Codes

The table below contains the rearrangement models codes that are recognized by GRAAu. Each code corresponds to a rearrangement model.

Rearrangement Model	Code
Reversal	R
Transposition	T
Reversal and Transposition	RT
Signed Reversal	SR
Signed Reversal and Transposition	SRT
Prefix Reversal	PR
Prefix Transposition	PT
Prefix Reversal and Prefix Transposition	PRPT
Signed Prefix Reversal	SPR
Signed Reversal, Transposition, and Signed Transreversal (A and B)	SRTTrAB
Signed Reversal, Transposition, and Signed Transreversal (A)	SRTTrA
Transposition and Signed Transreversal (A and B)	STTrAB
Signed Reversal, Transposition, and Signed Transreversal (B)	SRTTrB
Symmetric Reversal	SYR
Signed Symmetric Reversal	SSYR
Signed Almost Symmetric Reversal (asymmetry level 1)	SASYR1
Signed Almost Symmetric Reversal (asymmetry level 2)	SASYR2
Almost Symmetric Reversal (asymmetry level 1)	ASYR1
Almost Symmetric Reversal (asymmetry level 2)	ASYR2
Signed Almost Symmetric Reversal (asymmetry level 1) and Unitary Signed Reversal	SASYRUR1
Short Swap (Short Reversal)	ShSw
Prefix Reversal and Suffix Reversal	PRSR
Signed Prefix Reversal and Signed Suffix Reversal	SPRSSR
Prefix Reversal, Prefix Transposition, Suffix Reversal, and Suffix Transposition	PRPTSRST
Signed Prefix Reversal, Prefix Transposition, Signed Suffix Reversal, and Suffix Transposition	SPRPTSSRST
Signed Prefix Reversal and Prefix Transposition	SPRPT
Prefix Transposition and Suffix Transposition	PTST
Strip Move	SM
Prefix Strip Move	PSM
Prefix Strip Move and Suffix Strip Move	PSMSSM
Short Transposition	ShT
Short Reversal and Short Transposition	ShSwShT
Signed Short Reversal	SShSw
Signed Short Reversal and Short Transposition	SShSwShT
Reversal, Transposition, and Transreversal	RTTr
Super Short Cyclic Reversal	SuShCyR
Signed Super Short Cyclic Reversal	SSuShCyR
Signed Super Short Cyclic Reversal and Super Short Cyclic Transposition	SSuShCyRT
Super Short Reversal	SuShR
Signed Super Short Reversal	SSuShR
Signed Super Short Reversal and Super Short Transposition	SSuShRT