A Simple Java Sequence Alignment Editing Tool for Resolving Complex Repeat Regions.
- Author:
Seong Il HAM
1
;
Kyung Eun LEE
;
Hyun Seok PARK
Author Information
1. Institute of Bioinformatics, Macrogen Inc., Seoul, Korea. neo@ewha.ac.kr
- Publication Type:Note
- Keywords:
fragment assembly;
genome sequencing;
whole genome fragment assembly
- MeSH:
Genome;
Indonesia;
Pliability;
Sequence Alignment
- From:Genomics & Informatics
2009;7(1):46-48
- CountryRepublic of Korea
- Language:English
-
Abstract:
Finishing is the most time-consuming step in sequencing, and many genome projects are left unfinished due to complex repeat regions. Here, we have developed BACContigEditor, a prototype shotgun sequence finishing tool. It is essentially an editor that visualizes assemblies of shotgun sequence fragment reads as gapped multiple alignments. The program offers some flexibility that is needed to rapidly resolve complex regions within a working session. The sole purpose of the release is to promote collaborative creation of extensible software for fragment assembly editors, foster collaborative development, and reduce barriers to initial tool development effort. We describe our software architecture and identify current challenges. The program is available under an Open Source license.
