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Journal of Biomedicine and Biotechnology
Volume 2008 (2008), Article ID 675741, 7 pages
http://dx.doi.org/10.1155/2008/675741
Research Article

A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing

1 SmallSoft Co., Ltd., Jang-Dong 59-5, Yusung-Gu, Daejeon 305-343, South Korea
2Department of Computer Science and Engineering, Pusan National University, Busan 609-735, South Korea

Received 1 September 2007; Accepted 24 December 2007

Academic Editor: Daniel Howard

Copyright © 2008 Pan-Gyu Kim et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We have developed a Windows-based program, ConPath, as a scaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find the longest acyclic graphs. Using end read pairs of fixed-sized mate-pair libraries, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pair, and reports wrong assembly information by validating orientations and gap sizes. We have utilized ConPath in more than 10 microbial genome projects, including Mannheimia succiniciproducens and Vibro vulnificus, where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath. Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures.