Skip Navigation


Bioinformatics Advance Access originally published online on December 7, 2004
Bioinformatics 2005 21(8):1695-1698; doi:10.1093/bioinformatics/bti181
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/8/1695    most recent
bti181v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (3)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Li, W.
Right arrow Articles by Farman, M. L
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Li, W.
Right arrow Articles by Farman, M. L
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

TERMINUS—Telomeric End-Read Mining IN Unassembled Sequences

Weixi Li 1, Cathryn J. Rehmeyer 2, Chuck Staben 1 and Mark L Farman 2,*

1Department of Biological Sciences, University of Kentucky Lexington, KY 40546, USA
2Department of Plant Pathology, University of Kentucky Lexington, KY 40546, USA

*To whom correspondence should be addressed.

Summary: TERMINUS is a set of tools to map telomeres on draft sequences of whole genome shotgun sequencing projects. It mines raw sequence reads (from a trace archive) for telomeric reads, assembles them into contigs representing individual chromosome ends and BLASTs the resulting consensus sequences against the genome assembly to identify telomere-proximal genomic contigs. Finally, it estimates the sizes of telomeric gaps and identifies clones for gap closure. TERMINUS is implemented as a set of Perl scripts that requires two sets of inputs: the NCBI Trace Archive files for a given genome project; and ancillary genome assembly information. Results are output in spreadsheets containing information that facilitates manual validation.

Availability: The TERMINUS package and supplementary information can be downloaded from http://www.genome.kbrin.uky.edu/fungi_tel/terminus/

Contact: farman{at}uky.edu


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Appl. Environ. Microbiol.Home page
J. Lee, J. E. Jurgenson, J. F. Leslie, and R. L. Bowden
Alignment of Genetic and Physical Maps of Gibberella zeae
Appl. Envir. Microbiol., April 15, 2008; 74(8): 2349 - 2359.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
J. E. Galagan, M. R. Henn, L.-J. Ma, C. A. Cuomo, and B. Birren
Genomics of the fungal kingdom: Insights into eukaryotic biology
Genome Res., December 1, 2005; 15(12): 1620 - 1631.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.