W421 Using LTC software to assemble physical maps in complex genomes such as wheat

Date: Tuesday, January 17, 2012
Time: 1:30 PM
Room: Golden Ballroom
Zeev Frenkel , University of Haifa, Haifa, Israel
Etienne Paux , INRA, Clermont-Ferrand, France
David Mester , University of Haifa, Haifa, Israel
Catherine Feuillet , INRA, Clermont-Ferrand, France
Abraham Korol , University of Haifa, Haifa, Israel
Our Linear Topology Contig (LTC) program for contig assembly in physical mapping was created to overcome some limitations in the assembly by the standard FPC package. The program is able to automatically construct high quality contigs using BAC fingerprint data. It also can be used for manual editing, verifying, and merging of contigs based on information about markers found in BACs. In addition, LTC allows curing gaps, reviewing, reordering, and elongation of contigs obtained by other tools, e.g. by FPC package. In contrast to FPC that identifies false clone overlaps and chimerical clones using band map, LTC addresses these problems using network representation of clone overlaps. Our tests on real and simulated data show that LTC produces longer and more reliable contigs than FPC. The ordering of clones within LTC contigs is based on global optimization methods resulting in significant overlaps of adjacent clones that sometimes is not the case for FPC-based ordering. The objective of this presentation is to provide the trainees with detailed explanations on the main elements of LTC analysis. The training will be based on practice with simulated data based on published maize genome sequence. It will include the following main topics: (a) Main principles of LTC analysis; (b) Description of simulated data; (c) Installation and starting LTC program; (d) Input data format and importing of fingerprint data; (e) Automatic contig assembly and testing; (f) Output of LTC analysis; (g) Importing and verification contigs and MTPs assembled by FPC; (h) Quality control: resulted assembly vs. simulated clone position; (i) Elongation and merging of contigs; (j) Using LTC for identification of positive MTP clones from the list of positive 3D-pools with possible errors. LTC is available for Windows PC and for Linux PC with installed Wine software adapted to run VB applications.