![](/images/graphics-bg.png)
A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing
Joint Authors
Cho, Hwan-Gue
Kim, Pan-Gyu
Park, Kiejung
Source
Issue
Vol. 2008, Issue 2008 (31 Dec. 2008), pp.1-7, 7 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2007-01-09
Country of Publication
Egypt
No. of Pages
7
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Kim, Pan-Gyu& Cho, Hwan-Gue& Park, Kiejung. 2007. A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing. BioMed Research International،Vol. 2008, no. 2008, pp.1-7.
https://search.emarefa.net/detail/BIM-987793
Modern Language Association (MLA)
Kim, Pan-Gyu…[et al.]. A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing. BioMed Research International No. 2008 (2008), pp.1-7.
https://search.emarefa.net/detail/BIM-987793
American Medical Association (AMA)
Kim, Pan-Gyu& Cho, Hwan-Gue& Park, Kiejung. A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing. BioMed Research International. 2007. Vol. 2008, no. 2008, pp.1-7.
https://search.emarefa.net/detail/BIM-987793
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-987793