CORAL (Contig Ordering Algorithm)

An algorithm has been developed to order fingerprinted clones within contigs.

Project Description

About CORAL

   An algorithm has been developed to order fingerprinted clones within contigs. Current version of the CORAL algorithm is written in Java and embedded in iCE (Internet Contig Explorer v. 3.5 by Chris Fjell).  Stand-along version of CORAL also available.

Main features:

• variable tolerance
• band confirmation
• band accounting, shared bands
• canonical clones identification, based on “fat band” technology
• Two stages burying procedure
• Contig extension algorithm based on “best friend” determination
• Contig evaluation functions, based on quantity of unconfirmed bands in the middle clone, pairwise comparison and Sulston score
• ability to work with an FPC-file through iCE import-export functions

Testing results on different maps

Leishmania:

Hand-edited map:  983 canonical clones.

	Canonical clones	Common canonicals	Ordering mistakes
FPC-map	1915	866	46
CORALed map	994	839	12

JEC21:

Hand-edited map:  590 canonical clones.

	Canonical clones	Common canonicals	Ordering mistakes
FPC-map	1353	530	23
CORALed map	818	503	12

Poplar:

Hand-edited map:  2752 canonical clones.

	Canonical clones	Common canonicals	Ordering mistakes
FPC-map	4060	2609	88
CORALed map	2555	2554	29

Rhodococcus:

Hand-edited map: 1428 canonical clones.

	Canonical clones	Common canonicals	Ordering mistakes
FPC-map	3467	1321	110
CORALed map	1913	1026	26