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Title: Tools for comparative Genome Analysis by low redundant sequencing
P89
Lehmann, Rüdiger; Romualdi, Alessandro; Siddiqui, Roman; Szafranski, Karol; Glöckner, Gernot; Sühnel, Jürgen; Platzer, Matthias

rleh@imb-jena.de
Dept. of Genome Analysis and Dept. of Biocomputing, Institute of Molecular Biotechnology

Comparative genome analysis is a powerful tool for the identification of genetic variability between microorganisms. Ideally, the analysis is based on two or more completely sequenced genomes. A time and cost effective alternative is represented by the comparison of a completely sequenced reference genome to closely related target strains or species only characterised by low redundancy sequencing (3-5 x coverage).
For this purpose we are developing tools automatically analysing the low redun­dancy assembly of a target genome in consideration of the annotated reference. The results are summarised in user-friendly table formats hyper­linked with the details of the analysis.
For the assembly and edition of the shotgun sequences of the target genome we are using GAP4 (http://www.mrc-lmb.cam.ac.uk/pubseq/ftp/staden_package/) with the reference sequence as a backbone. The back­bone is provided with annotation and low quality values. In this way it has no influence on the consensus sequence which represents the target genome only.
At each point of the assembling or editing process, the consensus of the target genome can be analysed in respect of the annotation of the reference. The results are processed into HTML documents including graphical represen­tations of sequence coverage and quality. The detailed analysis includes the quality and coverage values for each deviation from the reference strain, compilations of identical and mutated genes, the kind of mutations etc. In addition, the results can be classified in user defined or established categories. All data are linked to the underlying nucleotide and amino acid sequences and their alignments.