Bacterial syntenies: an exact approach with gene quorum

BMC Bioinformatics

Table 1 Whole genomes alignement methods in the literature

			edition operations
Name	nb genomes	correspondence	INV/TRANS	DUPL	DEL	algorithm	reference
GRIMM	pairwise	one-to-one	yes	yes	yes	minimise evolutionary distance	[6]
CINTENY	pairwise	many-to-many	yes	yes	yes	minimise evolutionary distance	[7]
UNO AND TAGIURA	pairwise	one-to-one	yes	no	no	find common intervals	[8]
HEBER AND STOYE	multiple	one-to-one	yes	no	no	find common intervals	[9]
DIDIER	pairwise	many-to-many	yes	yes	no	find common intervals	[10]
GENE TEAMS	multiple	equivalence	yes	no	yes	divide and conquer	[11]
HOMOLOGY TEAMS	pairwise	equivalence	yes	yes	yes	divide and conquer	[12]
DOMAIN TEAMS	multiple	equivalence	yes	yes	yes	divide and conquer	[13]
MCGS	multiple	equivalence	yes	yes	yes	divide and conquer	[14]
MCPA GE	pairwise	equivalence	yes	yes	yes	divide and conquer	[15]
MCMU SE C	multiple	equivalence	yes	yes	yes	divide and conquer	[16]
C3PART	multiple	many-to-many	yes	yes	yes	partition the NAM	[17]
FISH	pairwise	many-to-many	local	no	yes	dynamic programming	[18]
DAGCHAINER	pairwise	many-to-many	no	no	yes	dynamic programming	[19]
COLINEAR SCAN	pairwise	many-to-many	no	no	yes	dynamic programming	[20]
SYNTENATOR	multiple	many-to-many	no	yes	yes	dynamic programming on POG	[21]
CYNTENATOR	multiple	many-to-many	no	yes	yes	same + phylogeny	[22]
ADHO RE	pairwise	many-to-many	no	tandem	yes	clustering	[30]
I-ADHO RE	multiple	many-to-many	no	tandem	yes	greedy heuristic	[26]

Principal approaches for whole genomes alignment and the search for syntenies. Note that the real goal of GRIMM and CINTENY is to reconstruct evolutionary scenarios, the extraction of syntenies is only a by-product of those algorithms. Note also that DOMAIN TEAMS uses a protein domain granularity, whereas all other methods operate at the gene level. Among the multiple comparison tools, MCGS (and its extension MCMU SE C), SYNTENATOR (and its extension CYNTENATOR) and I-ADHO RE can handle (directly or indirectly) a gene quorum.

ISSN: 1471-2105